From 550ae2e71e740e67911ed71ab77c4bef533ba5c9 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 17 Mar 2025 10:09:40 -0500 Subject: [PATCH 01/15] ci: Add containers_config workflow --- .github/workflows/containers_config.yml | 31 ++++++++++++ conf/containers/docker.config | 64 +++++++++++++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 .github/workflows/containers_config.yml create mode 100644 conf/containers/docker.config diff --git a/.github/workflows/containers_config.yml b/.github/workflows/containers_config.yml new file mode 100644 index 000000000..2e0b58a60 --- /dev/null +++ b/.github/workflows/containers_config.yml @@ -0,0 +1,31 @@ +name: CI + +on: + # FIXME Remove these and only run on release or PRs to main + push: + branches: [main,dev] + pull_request: + branches: [main,dev] + release: + types: [published] + # TODO workflow_dispatch: + +jobs: + build: + runs-on: ubuntu-latest + env: + FORCE_COLOR: 1 + # TODO matrix: + steps: + # TODO + # - uses: earthly/actions/setup-earthly@v1 + # with: + # version: v0.8.13 + - uses: actions/checkout@v2 + - uses: nf-core/setup-nextflow@v2 + with: + version: "25.01.0-edge" + - name: Snapshot containers + run: | + nextflow inspect . -profile wave,docker -format config > conf/containers/docker.config + diff --git a/conf/containers/docker.config b/conf/containers/docker.config new file mode 100644 index 000000000..f297d788d --- /dev/null +++ b/conf/containers/docker.config @@ -0,0 +1,64 @@ +process { withName: 'DUPRADAR' { container = 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--dcb3a3be56be6612' } } +process { withName: 'RSEM_PREPAREREFERENCE' { container = 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } +process { withName: 'FQ_SUBSAMPLE' { container = 'community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } +process { withName: 'FASTP' { container = 'community.wave.seqera.io/library/fastp:0.23.4--f8cefc1e5f7a782e' } } +process { withName: 'RSEQC_READDISTRIBUTION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'GTF_FILTER' { container = 'community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } +process { withName: 'DESEQ2_QC' { container = 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:d06fadc02f8422a2' } } +process { withName: 'GFFREAD' { container = 'community.wave.seqera.io/library/gffread:0.12.7--33b95f1cfcc0e572' } } +process { withName: 'RSEQC_READDUPLICATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera.io/library/picard:3.1.1--bae6cd265e6bf3d3' } } +process { withName: 'RSEM_MERGE_COUNTS' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } +process { withName: 'CAT_FASTQ' { container = 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' } } +process { withName: 'GUNZIP' { container = 'community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } +process { withName: 'KRAKEN2_KRAKEN2' { container = 'community.wave.seqera.io/library/kraken2_coreutils_pigz:0892e153c7954635' } } +process { withName: 'TXIMETA_TXIMPORT' { container = 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--cd025af46d4ef23a' } } +process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'UNTAR' { container = 'community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } +process { withName: 'HISAT2_BUILD' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } +process { withName: 'RSEQC_INNERDISTANCE' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'TRIMGALORE' { container = 'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d' } } +process { withName: 'BEDTOOLS_GENOMECOV' { container = 'community.wave.seqera.io/library/bedtools:2.31.1--7c4ce4cb07c09ee4' } } +process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065' } } +process { withName: 'RSEQC_BAMSTAT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'SORTMERNA' { container = 'community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' } } +process { withName: 'QUALIMAP_RNASEQ' { container = 'community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' } } +process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'STAR_ALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } +process { withName: 'SAMTOOLS_INDEX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'PRESEQ_LCEXTRAP' { container = 'community.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613' } } +process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29' } } +process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'UCSC_BEDCLIP' { container = 'community.wave.seqera.io/library/ucsc-bedclip:377--41de764ea1c26af4' } } +process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--f66c00635e28f216' } } +process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.27--b0d1ffb40dfd9e97' } } +process { withName: 'STAR_ALIGN_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } +process { withName: 'GTF2BED' { container = 'community.wave.seqera.io/library/perl:5.26.2--e6570c5f08d3e12c' } } +process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'community.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e' } } +process { withName: 'SALMON_INDEX' { container = 'community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } +process { withName: 'BRACKEN_BRACKEN' { container = 'community.wave.seqera.io/library/bracken:2.9--3d5af74ed6966fc1' } } +process { withName: 'UMITOOLS_EXTRACT' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'HISAT2_ALIGN' { container = 'community.wave.seqera.io/library/hisat2_samtools:9ef5e68250d2aa60' } } +process { withName: 'KALLISTO_INDEX' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } +process { withName: 'UMICOLLAPSE' { container = 'community.wave.seqera.io/library/umicollapse:1.1.0--74864b350c72f3a0' } } +process { withName: 'BBMAP_BBSPLIT' { container = 'community.wave.seqera.io/library/bbmap:39.10--168578230ff6490a' } } +process { withName: 'RSEQC_TIN' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'CUSTOM_TX2GENE' { container = 'community.wave.seqera.io/library/python:3.10.4--a643e28963f01eef' } } +process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'community.wave.seqera.io/library/python:3.12.2--8aba3d9ac529ff19' } } +process { withName: 'UMITOOLS_DEDUP' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'STRINGTIE_STRINGTIE' { container = 'community.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a' } } +process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } +process { withName: 'KALLISTO_QUANT' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } +process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } +process { withName: 'STAR_GENOMEGENERATE' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } +process { withName: 'SALMON_QUANT' { container = 'community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } +process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } +process { withName: 'FQ_LINT' { container = 'community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } +process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } +process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } From 4f3b895cb62caa2aedafa90016dea5e485b1fd0d Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 17 Mar 2025 10:23:25 -0500 Subject: [PATCH 02/15] ci: Give it a matrix --- .github/workflows/containers_config.yml | 12 ++++++++++-- ...{docker.config => containers_docker_amd64.config} | 0 2 files changed, 10 insertions(+), 2 deletions(-) rename conf/containers/{docker.config => containers_docker_amd64.config} (100%) diff --git a/.github/workflows/containers_config.yml b/.github/workflows/containers_config.yml index 2e0b58a60..3b2074503 100644 --- a/.github/workflows/containers_config.yml +++ b/.github/workflows/containers_config.yml @@ -15,7 +15,10 @@ jobs: runs-on: ubuntu-latest env: FORCE_COLOR: 1 - # TODO matrix: + strategy: + matrix: + container_type: ['docker', 'singularity'] # TODO , "singularity_oras"] + architecture: ['amd64', 'arm64'] steps: # TODO # - uses: earthly/actions/setup-earthly@v1 @@ -27,5 +30,10 @@ jobs: version: "25.01.0-edge" - name: Snapshot containers run: | - nextflow inspect . -profile wave,docker -format config > conf/containers/docker.config + if [ "${{ matrix.architecture }}" == "arm64" ]; then + profile="wave,${{ matrix.container_type }},arm" + else + profile="wave,${{ matrix.container_type }}" + fi + nextflow inspect . -profile $profile -format config > conf/containers/containers_${{ matrix.container_type }}_${{ matrix.architecture }}.config diff --git a/conf/containers/docker.config b/conf/containers/containers_docker_amd64.config similarity index 100% rename from conf/containers/docker.config rename to conf/containers/containers_docker_amd64.config From 7e606502d5874e68e7228efe1b578754c6292ff0 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 17 Mar 2025 11:21:58 -0500 Subject: [PATCH 03/15] ci: Update names --- .github/workflows/containers_config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/containers_config.yml b/.github/workflows/containers_config.yml index 3b2074503..267f3b2f3 100644 --- a/.github/workflows/containers_config.yml +++ b/.github/workflows/containers_config.yml @@ -1,4 +1,4 @@ -name: CI +name: Container Configs on: # FIXME Remove these and only run on release or PRs to main From b2b9a634c5bc5bb95847ee10b74a8e163afa2954 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 17 Mar 2025 11:32:38 -0500 Subject: [PATCH 04/15] ci: Add commit step --- .github/workflows/containers_config.yml | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/.github/workflows/containers_config.yml b/.github/workflows/containers_config.yml index 267f3b2f3..b98f78f06 100644 --- a/.github/workflows/containers_config.yml +++ b/.github/workflows/containers_config.yml @@ -1,7 +1,7 @@ name: Container Configs on: - # FIXME Remove these and only run on release or PRs to main + # FIXME Remove these and only run on release or PRs to main or TEMPLATE updates push: branches: [main,dev] pull_request: @@ -36,4 +36,14 @@ jobs: profile="wave,${{ matrix.container_type }}" fi nextflow inspect . -profile $profile -format config > conf/containers/containers_${{ matrix.container_type }}_${{ matrix.architecture }}.config + - name: Commit & push changes + id: commit-and-push + run: | + git config user.email "core@nf-co.re" + git config user.name "nf-core-bot" + git config push.default upstream + git add . + git status + git commit -m "[automated] Update container configs" + git push From 5e0f1f8089e77ae40be87d2bdb04c237405bceb1 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 17 Mar 2025 11:42:35 -0500 Subject: [PATCH 05/15] ci: Check out with bot auth token and just add containers --- .github/workflows/containers_config.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/containers_config.yml b/.github/workflows/containers_config.yml index b98f78f06..9162a9a8b 100644 --- a/.github/workflows/containers_config.yml +++ b/.github/workflows/containers_config.yml @@ -24,7 +24,10 @@ jobs: # - uses: earthly/actions/setup-earthly@v1 # with: # version: v0.8.13 - - uses: actions/checkout@v2 + # Use the @nf-core-bot token to check out so we can push later + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + with: + token: ${{ secrets.nf_core_bot_auth_token }} - uses: nf-core/setup-nextflow@v2 with: version: "25.01.0-edge" @@ -42,7 +45,7 @@ jobs: git config user.email "core@nf-co.re" git config user.name "nf-core-bot" git config push.default upstream - git add . + git add conf/containers/ git status git commit -m "[automated] Update container configs" git push From 901f4c3e49d1a3b672e28e6d51e822f22ea51361 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 17 Mar 2025 11:47:47 -0500 Subject: [PATCH 06/15] ci: Checkout pull request HEAD commit instead of merge commit --- .github/workflows/containers_config.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/containers_config.yml b/.github/workflows/containers_config.yml index 9162a9a8b..7826f24dd 100644 --- a/.github/workflows/containers_config.yml +++ b/.github/workflows/containers_config.yml @@ -28,6 +28,7 @@ jobs: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} + ref: ${{ github.event.pull_request.head.sha }} - uses: nf-core/setup-nextflow@v2 with: version: "25.01.0-edge" From 59fce993616dfd6e4da2a7bd6dead60ab3ae36ec Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 17 Mar 2025 11:58:59 -0500 Subject: [PATCH 07/15] ci: Try with head_ref --- .github/workflows/containers_config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/containers_config.yml b/.github/workflows/containers_config.yml index 7826f24dd..bafa64253 100644 --- a/.github/workflows/containers_config.yml +++ b/.github/workflows/containers_config.yml @@ -28,7 +28,7 @@ jobs: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} - ref: ${{ github.event.pull_request.head.sha }} + ref: ${{ github.head_ref }} - uses: nf-core/setup-nextflow@v2 with: version: "25.01.0-edge" From 33969d00caae85c2b49b5fddf10e7a0e36b83404 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 17 Mar 2025 13:25:46 -0500 Subject: [PATCH 08/15] ci: Add a . --- .github/workflows/containers_config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/containers_config.yml b/.github/workflows/containers_config.yml index bafa64253..9446271f7 100644 --- a/.github/workflows/containers_config.yml +++ b/.github/workflows/containers_config.yml @@ -46,7 +46,7 @@ jobs: git config user.email "core@nf-co.re" git config user.name "nf-core-bot" git config push.default upstream - git add conf/containers/ + git add conf/containers/. git status git commit -m "[automated] Update container configs" git push From 73e866bc91acd3809b0f5a6b27879c5c3048b075 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 17 Mar 2025 13:54:06 -0500 Subject: [PATCH 09/15] ci: Run containers snapshot in one step --- .github/workflows/containers_config.yml | 26 +++++++++++-------------- 1 file changed, 11 insertions(+), 15 deletions(-) diff --git a/.github/workflows/containers_config.yml b/.github/workflows/containers_config.yml index 9446271f7..53b692e7b 100644 --- a/.github/workflows/containers_config.yml +++ b/.github/workflows/containers_config.yml @@ -15,16 +15,7 @@ jobs: runs-on: ubuntu-latest env: FORCE_COLOR: 1 - strategy: - matrix: - container_type: ['docker', 'singularity'] # TODO , "singularity_oras"] - architecture: ['amd64', 'arm64'] steps: - # TODO - # - uses: earthly/actions/setup-earthly@v1 - # with: - # version: v0.8.13 - # Use the @nf-core-bot token to check out so we can push later - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -34,12 +25,17 @@ jobs: version: "25.01.0-edge" - name: Snapshot containers run: | - if [ "${{ matrix.architecture }}" == "arm64" ]; then - profile="wave,${{ matrix.container_type }},arm" - else - profile="wave,${{ matrix.container_type }}" - fi - nextflow inspect . -profile $profile -format config > conf/containers/containers_${{ matrix.container_type }}_${{ matrix.architecture }}.config + mkdir -p conf/containers + for container in docker singularity; do + for arch in amd64 arm64; do + if [ "$arch" = "arm64" ]; then + profile="wave,$container,arm" + else + profile="wave,$container" + fi + nextflow inspect . -profile $profile -format config > conf/containers/containers_${container}_${arch}.config + done + done - name: Commit & push changes id: commit-and-push run: | From 26179c70c4ad0935499fb38996e1ba3b66841a04 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 17 Mar 2025 14:00:01 -0500 Subject: [PATCH 10/15] ci: Sort the outputs ourselves --- .github/workflows/containers_config.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/containers_config.yml b/.github/workflows/containers_config.yml index 53b692e7b..e179c3b38 100644 --- a/.github/workflows/containers_config.yml +++ b/.github/workflows/containers_config.yml @@ -34,6 +34,8 @@ jobs: profile="wave,$container" fi nextflow inspect . -profile $profile -format config > conf/containers/containers_${container}_${arch}.config + echo "Created conf/containers/containers_${container}_${arch}.config" + sort -o conf/containers/containers_${container}_${arch}.config conf/containers/containers_${container}_${arch}.config done done - name: Commit & push changes From 51b089c857d2eb12a9110202f69f4df70feee712 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 17 Mar 2025 19:06:30 +0000 Subject: [PATCH 11/15] [automated] Update container configs --- .../containers/containers_docker_amd64.config | 104 +++++++++--------- .../containers/containers_docker_arm64.config | 64 +++++++++++ .../containers_singularity_amd64.config | 64 +++++++++++ .../containers_singularity_arm64.config | 64 +++++++++++ 4 files changed, 244 insertions(+), 52 deletions(-) create mode 100644 conf/containers/containers_docker_arm64.config create mode 100644 conf/containers/containers_singularity_amd64.config create mode 100644 conf/containers/containers_singularity_arm64.config diff --git a/conf/containers/containers_docker_amd64.config b/conf/containers/containers_docker_amd64.config index f297d788d..aca76f390 100644 --- a/conf/containers/containers_docker_amd64.config +++ b/conf/containers/containers_docker_amd64.config @@ -1,64 +1,64 @@ +process { withName: 'BBMAP_BBSPLIT' { container = 'community.wave.seqera.io/library/bbmap:39.10--168578230ff6490a' } } +process { withName: 'BEDTOOLS_GENOMECOV' { container = 'community.wave.seqera.io/library/bedtools:2.31.1--7c4ce4cb07c09ee4' } } +process { withName: 'BRACKEN_BRACKEN' { container = 'community.wave.seqera.io/library/bracken:2.9--3d5af74ed6966fc1' } } +process { withName: 'CAT_FASTQ' { container = 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' } } +process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'community.wave.seqera.io/library/python:3.12.2--8aba3d9ac529ff19' } } +process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'CUSTOM_TX2GENE' { container = 'community.wave.seqera.io/library/python:3.10.4--a643e28963f01eef' } } +process { withName: 'DESEQ2_QC' { container = 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:d06fadc02f8422a2' } } process { withName: 'DUPRADAR' { container = 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--dcb3a3be56be6612' } } -process { withName: 'RSEM_PREPAREREFERENCE' { container = 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } -process { withName: 'FQ_SUBSAMPLE' { container = 'community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } process { withName: 'FASTP' { container = 'community.wave.seqera.io/library/fastp:0.23.4--f8cefc1e5f7a782e' } } -process { withName: 'RSEQC_READDISTRIBUTION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'GTF_FILTER' { container = 'community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } -process { withName: 'DESEQ2_QC' { container = 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:d06fadc02f8422a2' } } +process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29' } } +process { withName: 'FQ_LINT' { container = 'community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } +process { withName: 'FQ_SUBSAMPLE' { container = 'community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } process { withName: 'GFFREAD' { container = 'community.wave.seqera.io/library/gffread:0.12.7--33b95f1cfcc0e572' } } -process { withName: 'RSEQC_READDUPLICATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera.io/library/picard:3.1.1--bae6cd265e6bf3d3' } } -process { withName: 'RSEM_MERGE_COUNTS' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } -process { withName: 'CAT_FASTQ' { container = 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' } } +process { withName: 'GTF2BED' { container = 'community.wave.seqera.io/library/perl:5.26.2--e6570c5f08d3e12c' } } +process { withName: 'GTF_FILTER' { container = 'community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } process { withName: 'GUNZIP' { container = 'community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } -process { withName: 'KRAKEN2_KRAKEN2' { container = 'community.wave.seqera.io/library/kraken2_coreutils_pigz:0892e153c7954635' } } -process { withName: 'TXIMETA_TXIMPORT' { container = 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--cd025af46d4ef23a' } } -process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'UNTAR' { container = 'community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } +process { withName: 'HISAT2_ALIGN' { container = 'community.wave.seqera.io/library/hisat2_samtools:9ef5e68250d2aa60' } } process { withName: 'HISAT2_BUILD' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } -process { withName: 'RSEQC_INNERDISTANCE' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'TRIMGALORE' { container = 'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d' } } -process { withName: 'BEDTOOLS_GENOMECOV' { container = 'community.wave.seqera.io/library/bedtools:2.31.1--7c4ce4cb07c09ee4' } } -process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065' } } -process { withName: 'RSEQC_BAMSTAT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'SORTMERNA' { container = 'community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' } } +process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } +process { withName: 'KALLISTO_INDEX' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } +process { withName: 'KALLISTO_QUANT' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } +process { withName: 'KRAKEN2_KRAKEN2' { container = 'community.wave.seqera.io/library/kraken2_coreutils_pigz:0892e153c7954635' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.27--b0d1ffb40dfd9e97' } } +process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } +process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera.io/library/picard:3.1.1--bae6cd265e6bf3d3' } } +process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } +process { withName: 'PRESEQ_LCEXTRAP' { container = 'community.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613' } } process { withName: 'QUALIMAP_RNASEQ' { container = 'community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' } } +process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } +process { withName: 'RSEM_MERGE_COUNTS' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } +process { withName: 'RSEM_PREPAREREFERENCE' { container = 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } +process { withName: 'RSEQC_BAMSTAT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } -process { withName: 'STAR_ALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } -process { withName: 'SAMTOOLS_INDEX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'PRESEQ_LCEXTRAP' { container = 'community.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613' } } -process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29' } } +process { withName: 'RSEQC_INNERDISTANCE' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'UCSC_BEDCLIP' { container = 'community.wave.seqera.io/library/ucsc-bedclip:377--41de764ea1c26af4' } } -process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--f66c00635e28f216' } } -process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.27--b0d1ffb40dfd9e97' } } -process { withName: 'STAR_ALIGN_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } -process { withName: 'GTF2BED' { container = 'community.wave.seqera.io/library/perl:5.26.2--e6570c5f08d3e12c' } } -process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'community.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e' } } -process { withName: 'SALMON_INDEX' { container = 'community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } -process { withName: 'BRACKEN_BRACKEN' { container = 'community.wave.seqera.io/library/bracken:2.9--3d5af74ed6966fc1' } } -process { withName: 'UMITOOLS_EXTRACT' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } -process { withName: 'HISAT2_ALIGN' { container = 'community.wave.seqera.io/library/hisat2_samtools:9ef5e68250d2aa60' } } -process { withName: 'KALLISTO_INDEX' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } -process { withName: 'UMICOLLAPSE' { container = 'community.wave.seqera.io/library/umicollapse:1.1.0--74864b350c72f3a0' } } -process { withName: 'BBMAP_BBSPLIT' { container = 'community.wave.seqera.io/library/bbmap:39.10--168578230ff6490a' } } +process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_READDISTRIBUTION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_READDUPLICATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } process { withName: 'RSEQC_TIN' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'SALMON_INDEX' { container = 'community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } +process { withName: 'SALMON_QUANT' { container = 'community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'CUSTOM_TX2GENE' { container = 'community.wave.seqera.io/library/python:3.10.4--a643e28963f01eef' } } -process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'community.wave.seqera.io/library/python:3.12.2--8aba3d9ac529ff19' } } -process { withName: 'UMITOOLS_DEDUP' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } -process { withName: 'STRINGTIE_STRINGTIE' { container = 'community.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a' } } -process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } -process { withName: 'KALLISTO_QUANT' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } +process { withName: 'SAMTOOLS_INDEX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SORTMERNA' { container = 'community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' } } +process { withName: 'STAR_ALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } +process { withName: 'STAR_ALIGN_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } process { withName: 'STAR_GENOMEGENERATE' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } -process { withName: 'SALMON_QUANT' { container = 'community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } -process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } -process { withName: 'FQ_LINT' { container = 'community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } -process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } -process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } +process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } +process { withName: 'STRINGTIE_STRINGTIE' { container = 'community.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a' } } +process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'community.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e' } } +process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065' } } +process { withName: 'TRIMGALORE' { container = 'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d' } } +process { withName: 'TXIMETA_TXIMPORT' { container = 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--cd025af46d4ef23a' } } +process { withName: 'UCSC_BEDCLIP' { container = 'community.wave.seqera.io/library/ucsc-bedclip:377--41de764ea1c26af4' } } +process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--f66c00635e28f216' } } +process { withName: 'UMICOLLAPSE' { container = 'community.wave.seqera.io/library/umicollapse:1.1.0--74864b350c72f3a0' } } +process { withName: 'UMITOOLS_DEDUP' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'UMITOOLS_EXTRACT' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'UNTAR' { container = 'community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } diff --git a/conf/containers/containers_docker_arm64.config b/conf/containers/containers_docker_arm64.config new file mode 100644 index 000000000..16fb4769b --- /dev/null +++ b/conf/containers/containers_docker_arm64.config @@ -0,0 +1,64 @@ +process { withName: 'BBMAP_BBSPLIT' { container = 'community.wave.seqera.io/library/bbmap:39.10--168578230ff6490a' } } +process { withName: 'BEDTOOLS_GENOMECOV' { container = 'community.wave.seqera.io/library/bedtools:2.31.1--7c4ce4cb07c09ee4' } } +process { withName: 'BRACKEN_BRACKEN' { container = 'community.wave.seqera.io/library/bracken:2.9--3d5af74ed6966fc1' } } +process { withName: 'CAT_FASTQ' { container = 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' } } +process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'community.wave.seqera.io/library/python:3.12.2--8aba3d9ac529ff19' } } +process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'CUSTOM_TX2GENE' { container = 'community.wave.seqera.io/library/python:3.10.4--a643e28963f01eef' } } +process { withName: 'DESEQ2_QC' { container = 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:d06fadc02f8422a2' } } +process { withName: 'DUPRADAR' { container = 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--dcb3a3be56be6612' } } +process { withName: 'FASTP' { container = 'community.wave.seqera.io/library/fastp:0.23.4--f8cefc1e5f7a782e' } } +process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29' } } +process { withName: 'FQ_LINT' { container = 'community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } +process { withName: 'FQ_SUBSAMPLE' { container = 'community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } +process { withName: 'GFFREAD' { container = 'community.wave.seqera.io/library/gffread:0.12.7--33b95f1cfcc0e572' } } +process { withName: 'GTF2BED' { container = 'community.wave.seqera.io/library/perl:5.26.2--e6570c5f08d3e12c' } } +process { withName: 'GTF_FILTER' { container = 'community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } +process { withName: 'GUNZIP' { container = 'community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } +process { withName: 'HISAT2_ALIGN' { container = 'community.wave.seqera.io/library/hisat2_samtools:9ef5e68250d2aa60' } } +process { withName: 'HISAT2_BUILD' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } +process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } +process { withName: 'KALLISTO_INDEX' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } +process { withName: 'KALLISTO_QUANT' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } +process { withName: 'KRAKEN2_KRAKEN2' { container = 'community.wave.seqera.io/library/kraken2_coreutils_pigz:0892e153c7954635' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.27--b0d1ffb40dfd9e97' } } +process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } +process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera.io/library/picard:3.1.1--bae6cd265e6bf3d3' } } +process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } +process { withName: 'PRESEQ_LCEXTRAP' { container = 'community.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613' } } +process { withName: 'QUALIMAP_RNASEQ' { container = 'community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' } } +process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'community.wave.seqera.io/library/rsem_star:5f8b7771e0edff1d' } } +process { withName: 'RSEM_MERGE_COUNTS' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } +process { withName: 'RSEM_PREPAREREFERENCE' { container = 'community.wave.seqera.io/library/rsem_star:5f8b7771e0edff1d' } } +process { withName: 'RSEQC_BAMSTAT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_INNERDISTANCE' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_READDISTRIBUTION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_READDUPLICATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_TIN' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'SALMON_INDEX' { container = 'community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } +process { withName: 'SALMON_QUANT' { container = 'community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } +process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SAMTOOLS_INDEX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SORTMERNA' { container = 'community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' } } +process { withName: 'STAR_ALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } +process { withName: 'STAR_ALIGN_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } +process { withName: 'STAR_GENOMEGENERATE' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } +process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:342c22574b6bb80b' } } +process { withName: 'STRINGTIE_STRINGTIE' { container = 'community.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a' } } +process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'community.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e' } } +process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065' } } +process { withName: 'TRIMGALORE' { container = 'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d' } } +process { withName: 'TXIMETA_TXIMPORT' { container = 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--cd025af46d4ef23a' } } +process { withName: 'UCSC_BEDCLIP' { container = 'community.wave.seqera.io/library/ucsc-bedclip:377--41de764ea1c26af4' } } +process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--f66c00635e28f216' } } +process { withName: 'UMICOLLAPSE' { container = 'community.wave.seqera.io/library/umicollapse:1.1.0--74864b350c72f3a0' } } +process { withName: 'UMITOOLS_DEDUP' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'UMITOOLS_EXTRACT' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'UNTAR' { container = 'community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } diff --git a/conf/containers/containers_singularity_amd64.config b/conf/containers/containers_singularity_amd64.config new file mode 100644 index 000000000..5c5b57da7 --- /dev/null +++ b/conf/containers/containers_singularity_amd64.config @@ -0,0 +1,64 @@ +process { withName: 'BBMAP_BBSPLIT' { container = 'docker://community.wave.seqera.io/library/bbmap:39.10--168578230ff6490a' } } +process { withName: 'BEDTOOLS_GENOMECOV' { container = 'docker://community.wave.seqera.io/library/bedtools:2.31.1--7c4ce4cb07c09ee4' } } +process { withName: 'BRACKEN_BRACKEN' { container = 'docker://community.wave.seqera.io/library/bracken:2.9--3d5af74ed6966fc1' } } +process { withName: 'CAT_FASTQ' { container = 'docker://community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' } } +process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'docker://community.wave.seqera.io/library/python:3.12.2--8aba3d9ac529ff19' } } +process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'CUSTOM_TX2GENE' { container = 'docker://community.wave.seqera.io/library/python:3.10.4--a643e28963f01eef' } } +process { withName: 'DESEQ2_QC' { container = 'docker://community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:d06fadc02f8422a2' } } +process { withName: 'DUPRADAR' { container = 'docker://community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--dcb3a3be56be6612' } } +process { withName: 'FASTP' { container = 'docker://community.wave.seqera.io/library/fastp:0.23.4--f8cefc1e5f7a782e' } } +process { withName: 'FASTQC' { container = 'docker://community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29' } } +process { withName: 'FQ_LINT' { container = 'docker://community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } +process { withName: 'FQ_SUBSAMPLE' { container = 'docker://community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } +process { withName: 'GFFREAD' { container = 'docker://community.wave.seqera.io/library/gffread:0.12.7--33b95f1cfcc0e572' } } +process { withName: 'GTF2BED' { container = 'docker://community.wave.seqera.io/library/perl:5.26.2--e6570c5f08d3e12c' } } +process { withName: 'GTF_FILTER' { container = 'docker://community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } +process { withName: 'GUNZIP' { container = 'docker://community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } +process { withName: 'HISAT2_ALIGN' { container = 'docker://community.wave.seqera.io/library/hisat2_samtools:9ef5e68250d2aa60' } } +process { withName: 'HISAT2_BUILD' { container = 'docker://community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } +process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'docker://community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } +process { withName: 'KALLISTO_INDEX' { container = 'docker://community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } +process { withName: 'KALLISTO_QUANT' { container = 'docker://community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } +process { withName: 'KRAKEN2_KRAKEN2' { container = 'docker://community.wave.seqera.io/library/kraken2_coreutils_pigz:0892e153c7954635' } } +process { withName: 'MULTIQC' { container = 'docker://community.wave.seqera.io/library/multiqc:1.27--b0d1ffb40dfd9e97' } } +process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'docker://community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } +process { withName: 'PICARD_MARKDUPLICATES' { container = 'docker://community.wave.seqera.io/library/picard:3.1.1--bae6cd265e6bf3d3' } } +process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'docker://community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } +process { withName: 'PRESEQ_LCEXTRAP' { container = 'docker://community.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613' } } +process { withName: 'QUALIMAP_RNASEQ' { container = 'docker://community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' } } +process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'docker://community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } +process { withName: 'RSEM_MERGE_COUNTS' { container = 'docker://community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } +process { withName: 'RSEM_PREPAREREFERENCE' { container = 'docker://community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } +process { withName: 'RSEQC_BAMSTAT' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_INNERDISTANCE' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_READDISTRIBUTION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_READDUPLICATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_TIN' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'SALMON_INDEX' { container = 'docker://community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } +process { withName: 'SALMON_QUANT' { container = 'docker://community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } +process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SAMTOOLS_IDXSTATS' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SAMTOOLS_INDEX' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SAMTOOLS_SORT' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SAMTOOLS_STATS' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SORTMERNA' { container = 'docker://community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' } } +process { withName: 'STAR_ALIGN' { container = 'docker://community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } +process { withName: 'STAR_ALIGN_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } +process { withName: 'STAR_GENOMEGENERATE' { container = 'docker://community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } +process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } +process { withName: 'STRINGTIE_STRINGTIE' { container = 'docker://community.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a' } } +process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'docker://community.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e' } } +process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'docker://community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065' } } +process { withName: 'TRIMGALORE' { container = 'docker://community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d' } } +process { withName: 'TXIMETA_TXIMPORT' { container = 'docker://community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--cd025af46d4ef23a' } } +process { withName: 'UCSC_BEDCLIP' { container = 'docker://community.wave.seqera.io/library/ucsc-bedclip:377--41de764ea1c26af4' } } +process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'docker://community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--f66c00635e28f216' } } +process { withName: 'UMICOLLAPSE' { container = 'docker://community.wave.seqera.io/library/umicollapse:1.1.0--74864b350c72f3a0' } } +process { withName: 'UMITOOLS_DEDUP' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'UMITOOLS_EXTRACT' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'UNTAR' { container = 'docker://community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } diff --git a/conf/containers/containers_singularity_arm64.config b/conf/containers/containers_singularity_arm64.config new file mode 100644 index 000000000..032c75222 --- /dev/null +++ b/conf/containers/containers_singularity_arm64.config @@ -0,0 +1,64 @@ +process { withName: 'BBMAP_BBSPLIT' { container = 'docker://community.wave.seqera.io/library/bbmap:39.10--168578230ff6490a' } } +process { withName: 'BEDTOOLS_GENOMECOV' { container = 'docker://community.wave.seqera.io/library/bedtools:2.31.1--7c4ce4cb07c09ee4' } } +process { withName: 'BRACKEN_BRACKEN' { container = 'docker://community.wave.seqera.io/library/bracken:2.9--3d5af74ed6966fc1' } } +process { withName: 'CAT_FASTQ' { container = 'docker://community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' } } +process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'docker://community.wave.seqera.io/library/python:3.12.2--8aba3d9ac529ff19' } } +process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'CUSTOM_TX2GENE' { container = 'docker://community.wave.seqera.io/library/python:3.10.4--a643e28963f01eef' } } +process { withName: 'DESEQ2_QC' { container = 'docker://community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:d06fadc02f8422a2' } } +process { withName: 'DUPRADAR' { container = 'docker://community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--dcb3a3be56be6612' } } +process { withName: 'FASTP' { container = 'docker://community.wave.seqera.io/library/fastp:0.23.4--f8cefc1e5f7a782e' } } +process { withName: 'FASTQC' { container = 'docker://community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29' } } +process { withName: 'FQ_LINT' { container = 'docker://community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } +process { withName: 'FQ_SUBSAMPLE' { container = 'docker://community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } +process { withName: 'GFFREAD' { container = 'docker://community.wave.seqera.io/library/gffread:0.12.7--33b95f1cfcc0e572' } } +process { withName: 'GTF2BED' { container = 'docker://community.wave.seqera.io/library/perl:5.26.2--e6570c5f08d3e12c' } } +process { withName: 'GTF_FILTER' { container = 'docker://community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } +process { withName: 'GUNZIP' { container = 'docker://community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } +process { withName: 'HISAT2_ALIGN' { container = 'docker://community.wave.seqera.io/library/hisat2_samtools:9ef5e68250d2aa60' } } +process { withName: 'HISAT2_BUILD' { container = 'docker://community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } +process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'docker://community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } +process { withName: 'KALLISTO_INDEX' { container = 'docker://community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } +process { withName: 'KALLISTO_QUANT' { container = 'docker://community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } +process { withName: 'KRAKEN2_KRAKEN2' { container = 'docker://community.wave.seqera.io/library/kraken2_coreutils_pigz:0892e153c7954635' } } +process { withName: 'MULTIQC' { container = 'docker://community.wave.seqera.io/library/multiqc:1.27--b0d1ffb40dfd9e97' } } +process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'docker://community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } +process { withName: 'PICARD_MARKDUPLICATES' { container = 'docker://community.wave.seqera.io/library/picard:3.1.1--bae6cd265e6bf3d3' } } +process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'docker://community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } +process { withName: 'PRESEQ_LCEXTRAP' { container = 'docker://community.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613' } } +process { withName: 'QUALIMAP_RNASEQ' { container = 'docker://community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' } } +process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'docker://community.wave.seqera.io/library/rsem_star:5f8b7771e0edff1d' } } +process { withName: 'RSEM_MERGE_COUNTS' { container = 'docker://community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } +process { withName: 'RSEM_PREPAREREFERENCE' { container = 'docker://community.wave.seqera.io/library/rsem_star:5f8b7771e0edff1d' } } +process { withName: 'RSEQC_BAMSTAT' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_INNERDISTANCE' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_READDISTRIBUTION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_READDUPLICATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'RSEQC_TIN' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } +process { withName: 'SALMON_INDEX' { container = 'docker://community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } +process { withName: 'SALMON_QUANT' { container = 'docker://community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } +process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SAMTOOLS_IDXSTATS' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SAMTOOLS_INDEX' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SAMTOOLS_SORT' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SAMTOOLS_STATS' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } +process { withName: 'SORTMERNA' { container = 'docker://community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' } } +process { withName: 'STAR_ALIGN' { container = 'docker://community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } +process { withName: 'STAR_ALIGN_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } +process { withName: 'STAR_GENOMEGENERATE' { container = 'docker://community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } +process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:342c22574b6bb80b' } } +process { withName: 'STRINGTIE_STRINGTIE' { container = 'docker://community.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a' } } +process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'docker://community.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e' } } +process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'docker://community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065' } } +process { withName: 'TRIMGALORE' { container = 'docker://community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d' } } +process { withName: 'TXIMETA_TXIMPORT' { container = 'docker://community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--cd025af46d4ef23a' } } +process { withName: 'UCSC_BEDCLIP' { container = 'docker://community.wave.seqera.io/library/ucsc-bedclip:377--41de764ea1c26af4' } } +process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'docker://community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--f66c00635e28f216' } } +process { withName: 'UMICOLLAPSE' { container = 'docker://community.wave.seqera.io/library/umicollapse:1.1.0--74864b350c72f3a0' } } +process { withName: 'UMITOOLS_DEDUP' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'UMITOOLS_EXTRACT' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } +process { withName: 'UNTAR' { container = 'docker://community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } From 3a7cff2b0b1aa305d57faa2734af1a0026424f77 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 17 Mar 2025 14:05:34 -0500 Subject: [PATCH 12/15] build: Try locking down some containers --- conf/arm.config | 273 ------------------------------------------------ nextflow.config | 5 +- 2 files changed, 4 insertions(+), 274 deletions(-) delete mode 100644 conf/arm.config diff --git a/conf/arm.config b/conf/arm.config deleted file mode 100644 index bb5b222c3..000000000 --- a/conf/arm.config +++ /dev/null @@ -1,273 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running the pipeline with ARM architecture -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines custom containers and Conda definitions required to run pipeline with ARM. - - Use as follows: - nextflow run nf-core/rnaseq -profile ,arm - ----------------------------------------------------------------------------------------- -*/ - -process { - - // - // Tools that have native Conda builds for AMD and ARM - // - - withName: 'BBMAP_BBSPLIT' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/63ca91c8bf7285296777de219e5d5a71d2a7de47599cbc94441aced7868a4f83/data' : 'community.wave.seqera.io/library/bbmap:39.10--908996c2fb304bec' } - } - - withName: 'BEDTOOLS_GENOMECOV' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/519a920dacc643078823740486c40d30b9f555c493217d9f72db04901350e009/data' : 'community.wave.seqera.io/library/bedtools:2.31.1--efd79503b8c63422' } - } - - withName: 'BRACKEN_BRACKEN' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/64/648fd6bc2805481aa60db7ee9e37d41d7643eaaabd92f21bf1019f8b3f0879a6/data' : 'community.wave.seqera.io/library/bracken:3.1--0b6ab6dde7667f60' } - } - - withName: 'CAT_FASTQ' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/38d3638640600b355110f9bca56c514e3cc068bf96b8b68f98cba2a59a053505/data' : 'community.wave.seqera.io/library/coreutils:9.5--3931e2d27d9884e5' } - } - - withName: 'CUSTOM_CATADDITIONALFASTA' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c1/c17acd739990ad12c06583f57b097014c2bde5a91d0977fd102864a82f95e136/data' : 'community.wave.seqera.io/library/python:3.12.2--0d47e6fe32e00784' } - } - - withName: 'CUSTOM_GETCHROMSIZES' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } - } - - withName: 'CUSTOM_TX2GENE' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/60/6029f43341dc0bea31d14c2ce4c779d7a48dfed6ecb29ce1630b8378c560c490/data' : 'community.wave.seqera.io/library/python:3.10.4--d0dc5eb8ea72fa82' } - } - - withName: 'DESEQ2_QC' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/70/70a3d17733d2c21cff464c31a7a57438cea528bea84c675b7c474eaa7f075f57/data' : 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:8bd3e9db55b129d7' } - } - - withName: 'DUPRADAR' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10141f8fd43964316d04214a5f7d99a62e11cdbab5bd2fcd4f7c3c06eca9f2f6/data' : 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--f75495d6abf45328' } - } - - withName: 'FASTP' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7e/7ec6234f24305b9694b89de0352fff942ce1d68f840184020b0b9135bc54bda1/data' : 'community.wave.seqera.io/library/fastp:0.23.4--c1051f83dcae53f5' } - } - - withName: 'FASTQC' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fd/fd39534bf298698cbe3ee4d4a6f1e73330ec4bca44c38dd9a4d06cb5ea838017/data' : 'community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a' } - } - - withName: 'FQ_SUBSAMPLE' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b00189d4f7eed55199354a3dff8a9a535e1dfb3a2f4c97f5d0bf9e388105795e/data' : 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } - } - - withName: 'GFFREAD' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9e6db95013607b07689e38ee37a654d029236de77fdfde97fe1866f45d01e064/data' : 'community.wave.seqera.io/library/gffread:0.12.7--1577aa7c95340d9f' } - } - - withName: 'GTF2BED' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/89/896a3e55b2f664def0f8707420e1f53b4c447adb99fd6a1432a155c3403b9199/data' : 'community.wave.seqera.io/library/perl:5.26.2--2a6adf51d600e047' } - } - - withName: 'GTF_FILTER' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } - } - - withName: 'GUNZIP' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } - } - - withName: 'HISAT2_ALIGN' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/95/95a04506094435ef9cbd94b479d5cd713cd1d106d5e5718bf4410686c3d19f15/data' : 'community.wave.seqera.io/library/hisat2_samtools:aaedc5f7a0ece7e8' } - } - - withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/95/95a04506094435ef9cbd94b479d5cd713cd1d106d5e5718bf4410686c3d19f15/data' : 'community.wave.seqera.io/library/hisat2_samtools:aaedc5f7a0ece7e8' } - } - - withName: 'KALLISTO_INDEX' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24655791b5db39ffdfffa8e5aeabfd11dda4553b5311ddb22e724c38b1591e8d/data' : 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } - } - - withName: 'KALLISTO_QUANT' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24655791b5db39ffdfffa8e5aeabfd11dda4553b5311ddb22e724c38b1591e8d/data' : 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } - } - - withName: 'KRAKEN2_KRAKEN2' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/beba752dd6b17d3dd79b9a71dd2c1c46d09fa1e28212b6aef7c6119d68804f4a/data' : 'community.wave.seqera.io/library/kraken2_coreutils_pigz:2a28cee7c0427b32' } - } - - withName: 'MULTIQC' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6e/6e97dcafc5915f90f863e70153f96bbe47963ebfd08383454d8bcd7263696e4e/data' : 'community.wave.seqera.io/library/multiqc:1.25.1--4062a515975cacba' } - } - - withName: 'MULTIQC_CUSTOM_BIOTYPE' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } - } - - withName: 'PICARD_MARKDUPLICATES' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c0d4bbb10417a70d137a28da09329d9f9fbdf964a1cfeda24b05b618cae6b16f/data' : 'community.wave.seqera.io/library/picard:3.1.1--c28da730a329ab3c' } - } - - withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4ad78019c37ff4ab22c0dff6ab1af655c6438562ef644d0323861a97971d7694/data' : 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } - } - - withName: 'PRESEQ_LCEXTRAP' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5ab535d5b4c88dc4837cab00919d4d5ea66dd4d6dc837d841886bef72145f435/data' : 'community.wave.seqera.io/library/preseq:3.2.0--80c9d2ffee38d3ac' } - } - - withName: 'QUALIMAP_RNASEQ' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7a/7aa0998788d327c6e7104c2c1e7bea2e8bb8fb7076ec5de3fdab4027e501b9a9/data' : 'community.wave.seqera.io/library/qualimap:2.3--8375b60bba97a2a6' } - } - - withName: 'RSEM_CALCULATEEXPRESSION' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } - } - - withName: 'RSEM_MERGE_COUNTS' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4ad78019c37ff4ab22c0dff6ab1af655c6438562ef644d0323861a97971d7694/data' : 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } - } - - withName: 'RSEM_PREPAREREFERENCE' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } - } - - withName: 'RSEQC_BAMSTAT' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } - } - - withName: 'RSEQC_INFEREXPERIMENT' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } - } - - withName: 'RSEQC_INNERDISTANCE' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } - } - - withName: 'RSEQC_JUNCTIONANNOTATION' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } - } - - withName: 'RSEQC_JUNCTIONSATURATION' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } - } - - withName: 'RSEQC_READDISTRIBUTION' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } - } - - withName: 'RSEQC_READDUPLICATION' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } - } - - withName: 'RSEQC_TIN' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } - } - - withName: 'SALMON_INDEX' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b8/b8e3bcb1daa42497d0159cd5ae3b6d164b4470a972dd72d9d10b365fa166e5a4/data' : 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } - } - - withName: 'SALMON_QUANT' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b8/b8e3bcb1daa42497d0159cd5ae3b6d164b4470a972dd72d9d10b365fa166e5a4/data' : 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } - } - - withName: 'SAMTOOLS_FLAGSTAT' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } - } - - withName: 'SAMTOOLS_IDXSTATS' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } - } - - withName: 'SAMTOOLS_INDEX' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } - } - - withName: 'SAMTOOLS_SORT' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } - } - - withName: 'SAMTOOLS_STATS' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } - } - - withName: 'STAR_ALIGN' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/40/40d803371e50330de0773c7cc50315e2c3b4b41dcf123823adeb0a07d71654c1/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' } - } - - withName: 'STAR_GENOMEGENERATE' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/40/40d803371e50330de0773c7cc50315e2c3b4b41dcf123823adeb0a07d71654c1/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' } - } - - withName: 'STRINGTIE_STRINGTIE' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9ebc6b1a27262420a5739330d369086b0d8c941a43b81d3fd0f741045bb3d46f/data' : 'community.wave.seqera.io/library/stringtie:2.2.3--77d8df3265c94ba1' } - } - - withName: 'SUBREAD_FEATURECOUNTS' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2a/2a81571bc8c4ac812adb76c51045a245041d7cc8923a2d7cc34a866588fead0c/data' : 'community.wave.seqera.io/library/subread:2.0.6--df9c6b502b57bb9c' } - } - - withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a7/a7d1ef576617b9790973bc9d178c4ef136a52b6337260c536cff6cd68f103b45/data' : 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--859858039875a2a5' } - } - - withName: 'TRIMGALORE' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10e7b91ef06bdf5790120809afc8cf36aac0261b618d810c952d5afd60dd5ed2/data' : 'community.wave.seqera.io/library/cutadapt_trim-galore:2aa2fc797328573b' } - } - - withName: 'TXIMETA_TXIMPORT' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f8/f89ab1fef6e38e572ad1844d06f6d3d334d2b19a70c9e5d87bfc862b88728c23/data' : 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--3b0ca8a1710e2b2b' } - } - - withName: 'UCSC_BEDCLIP' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5f/5f559cabdfda8b2937c4213d3a53547eb882b2fc8cc36ebfeff07481fa47823a/data' : 'community.wave.seqera.io/library/ucsc-bedclip:377--489576e83f1992e0' } - } - - withName: 'UCSC_BEDGRAPHTOBIGWIG' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/389312a4a6022c5f5d2510dfa9bedb0491b36c8a27e8d842c05de00bc3b5be76/data' : 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--1db18e1b19f8e5f1' } - } - - withName: 'UMITOOLS_DEDUP' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } - } - - withName: 'UMITOOLS_EXTRACT' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } - } - - withName: 'UMITOOLS_PREPAREFORRSEM' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } - } - - withName: 'UNTAR' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } - } - - // SortMeRNA does not yet have aarch64 builds conda forge. Working on it, using builds from Seqera channel for now - // See https://github.com/conda-forge/conda-forge-pinning-feedstock/pull/7454 - - withName: 'SORTMERNA' { - conda = 'seqera::sortmerna=4.3.7' - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f1/f161ea3d4083b7d8fcbf8524cb5ab69f386b4e36b771bb5abf9ccf8ab29e9775/data' : 'community.wave.seqera.io/library/sortmerna:4.3.7--4cc83a7bffbaaa61' } - } - - // - // Tools that do not have native Conda builds for AMD and ARM. Required custom builds in 'seqera' Conda channel. - // - - withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' } - } - - withName: 'STAR_GENOMEGENERATE_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' } - } - -} diff --git a/nextflow.config b/nextflow.config index 1e1a5ed7f..f58243326 100644 --- a/nextflow.config +++ b/nextflow.config @@ -182,6 +182,7 @@ profiles { apptainer.enabled = false } docker { + includeConfig 'conf/containers/containers_docker_amd64.config' docker.enabled = true conda.enabled = false singularity.enabled = false @@ -192,10 +193,12 @@ profiles { docker.runOptions = '-u $(id -u):$(id -g)' } arm { + // TODO: Handle docker_arm, singularity_arm, etc. + includeConfig 'conf/containers/containers_docker_arm64.config' docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' - includeConfig 'conf/arm.config' } singularity { + includeConfig 'conf/containers/containers_singularity_amd64.config' singularity.enabled = true singularity.autoMounts = true conda.enabled = false From e6d7871df10e14a1a49e2d7cedc64892f46734fe Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 17 Mar 2025 19:12:00 +0000 Subject: [PATCH 13/15] [automated] Update container configs --- conf/containers/containers_docker_arm64.config | 6 +++--- conf/containers/containers_singularity_arm64.config | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/conf/containers/containers_docker_arm64.config b/conf/containers/containers_docker_arm64.config index 16fb4769b..aca76f390 100644 --- a/conf/containers/containers_docker_arm64.config +++ b/conf/containers/containers_docker_arm64.config @@ -27,9 +27,9 @@ process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } process { withName: 'PRESEQ_LCEXTRAP' { container = 'community.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613' } } process { withName: 'QUALIMAP_RNASEQ' { container = 'community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' } } -process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'community.wave.seqera.io/library/rsem_star:5f8b7771e0edff1d' } } +process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } process { withName: 'RSEM_MERGE_COUNTS' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } -process { withName: 'RSEM_PREPAREREFERENCE' { container = 'community.wave.seqera.io/library/rsem_star:5f8b7771e0edff1d' } } +process { withName: 'RSEM_PREPAREREFERENCE' { container = 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } process { withName: 'RSEQC_BAMSTAT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } process { withName: 'RSEQC_INNERDISTANCE' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } @@ -49,7 +49,7 @@ process { withName: 'SORTMERNA' { container = 'community.wave.seqera.io/library/ process { withName: 'STAR_ALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } process { withName: 'STAR_ALIGN_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } process { withName: 'STAR_GENOMEGENERATE' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } -process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:342c22574b6bb80b' } } +process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } process { withName: 'STRINGTIE_STRINGTIE' { container = 'community.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a' } } process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'community.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e' } } process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065' } } diff --git a/conf/containers/containers_singularity_arm64.config b/conf/containers/containers_singularity_arm64.config index 032c75222..5c5b57da7 100644 --- a/conf/containers/containers_singularity_arm64.config +++ b/conf/containers/containers_singularity_arm64.config @@ -27,9 +27,9 @@ process { withName: 'PICARD_MARKDUPLICATES' { container = 'docker://community.wa process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'docker://community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } process { withName: 'PRESEQ_LCEXTRAP' { container = 'docker://community.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613' } } process { withName: 'QUALIMAP_RNASEQ' { container = 'docker://community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' } } -process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'docker://community.wave.seqera.io/library/rsem_star:5f8b7771e0edff1d' } } +process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'docker://community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } process { withName: 'RSEM_MERGE_COUNTS' { container = 'docker://community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } -process { withName: 'RSEM_PREPAREREFERENCE' { container = 'docker://community.wave.seqera.io/library/rsem_star:5f8b7771e0edff1d' } } +process { withName: 'RSEM_PREPAREREFERENCE' { container = 'docker://community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } process { withName: 'RSEQC_BAMSTAT' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } process { withName: 'RSEQC_INNERDISTANCE' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } @@ -49,7 +49,7 @@ process { withName: 'SORTMERNA' { container = 'docker://community.wave.seqera.io process { withName: 'STAR_ALIGN' { container = 'docker://community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } process { withName: 'STAR_ALIGN_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } process { withName: 'STAR_GENOMEGENERATE' { container = 'docker://community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } -process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:342c22574b6bb80b' } } +process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } process { withName: 'STRINGTIE_STRINGTIE' { container = 'docker://community.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a' } } process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'docker://community.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e' } } process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'docker://community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065' } } From 9e22ce27fa6db451198ba3e4b8492f070440e985 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 25 Mar 2025 15:46:17 -0500 Subject: [PATCH 14/15] build: Rename arm profile to apple and make a real arm profile Update container versions for ARM architecture and --- .../containers/containers_docker_arm64.config | 128 +++++++++--------- .../containers_singularity_arm64.config | 128 +++++++++--------- nextflow.config | 11 +- 3 files changed, 134 insertions(+), 133 deletions(-) diff --git a/conf/containers/containers_docker_arm64.config b/conf/containers/containers_docker_arm64.config index aca76f390..f4e5fa426 100644 --- a/conf/containers/containers_docker_arm64.config +++ b/conf/containers/containers_docker_arm64.config @@ -1,64 +1,64 @@ -process { withName: 'BBMAP_BBSPLIT' { container = 'community.wave.seqera.io/library/bbmap:39.10--168578230ff6490a' } } -process { withName: 'BEDTOOLS_GENOMECOV' { container = 'community.wave.seqera.io/library/bedtools:2.31.1--7c4ce4cb07c09ee4' } } -process { withName: 'BRACKEN_BRACKEN' { container = 'community.wave.seqera.io/library/bracken:2.9--3d5af74ed6966fc1' } } -process { withName: 'CAT_FASTQ' { container = 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' } } -process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'community.wave.seqera.io/library/python:3.12.2--8aba3d9ac529ff19' } } -process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'CUSTOM_TX2GENE' { container = 'community.wave.seqera.io/library/python:3.10.4--a643e28963f01eef' } } -process { withName: 'DESEQ2_QC' { container = 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:d06fadc02f8422a2' } } -process { withName: 'DUPRADAR' { container = 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--dcb3a3be56be6612' } } -process { withName: 'FASTP' { container = 'community.wave.seqera.io/library/fastp:0.23.4--f8cefc1e5f7a782e' } } -process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29' } } -process { withName: 'FQ_LINT' { container = 'community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } -process { withName: 'FQ_SUBSAMPLE' { container = 'community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } -process { withName: 'GFFREAD' { container = 'community.wave.seqera.io/library/gffread:0.12.7--33b95f1cfcc0e572' } } -process { withName: 'GTF2BED' { container = 'community.wave.seqera.io/library/perl:5.26.2--e6570c5f08d3e12c' } } -process { withName: 'GTF_FILTER' { container = 'community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } -process { withName: 'GUNZIP' { container = 'community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } -process { withName: 'HISAT2_ALIGN' { container = 'community.wave.seqera.io/library/hisat2_samtools:9ef5e68250d2aa60' } } -process { withName: 'HISAT2_BUILD' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } -process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } -process { withName: 'KALLISTO_INDEX' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } -process { withName: 'KALLISTO_QUANT' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } -process { withName: 'KRAKEN2_KRAKEN2' { container = 'community.wave.seqera.io/library/kraken2_coreutils_pigz:0892e153c7954635' } } -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.27--b0d1ffb40dfd9e97' } } -process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } -process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera.io/library/picard:3.1.1--bae6cd265e6bf3d3' } } -process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } -process { withName: 'PRESEQ_LCEXTRAP' { container = 'community.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613' } } -process { withName: 'QUALIMAP_RNASEQ' { container = 'community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' } } -process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } -process { withName: 'RSEM_MERGE_COUNTS' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } -process { withName: 'RSEM_PREPAREREFERENCE' { container = 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } -process { withName: 'RSEQC_BAMSTAT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_INNERDISTANCE' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_READDISTRIBUTION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_READDUPLICATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_TIN' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'SALMON_INDEX' { container = 'community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } -process { withName: 'SALMON_QUANT' { container = 'community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } -process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'SAMTOOLS_INDEX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'SORTMERNA' { container = 'community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' } } -process { withName: 'STAR_ALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } -process { withName: 'STAR_ALIGN_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } -process { withName: 'STAR_GENOMEGENERATE' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } -process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } -process { withName: 'STRINGTIE_STRINGTIE' { container = 'community.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a' } } -process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'community.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e' } } -process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065' } } -process { withName: 'TRIMGALORE' { container = 'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d' } } -process { withName: 'TXIMETA_TXIMPORT' { container = 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--cd025af46d4ef23a' } } -process { withName: 'UCSC_BEDCLIP' { container = 'community.wave.seqera.io/library/ucsc-bedclip:377--41de764ea1c26af4' } } -process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--f66c00635e28f216' } } -process { withName: 'UMICOLLAPSE' { container = 'community.wave.seqera.io/library/umicollapse:1.1.0--74864b350c72f3a0' } } -process { withName: 'UMITOOLS_DEDUP' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } -process { withName: 'UMITOOLS_EXTRACT' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } -process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } -process { withName: 'UNTAR' { container = 'community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } +process { withName: 'BBMAP_BBSPLIT' { container = 'community.wave.seqera.io/library/bbmap:39.10--908996c2fb304bec' } } +process { withName: 'BEDTOOLS_GENOMECOV' { container = 'community.wave.seqera.io/library/bedtools:2.31.1--efd79503b8c63422' } } +process { withName: 'BRACKEN_BRACKEN' { container = 'community.wave.seqera.io/library/bracken:2.9--e06b532ae215c74d' } } +process { withName: 'CAT_FASTQ' { container = 'community.wave.seqera.io/library/coreutils:9.5--3931e2d27d9884e5' } } +process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'community.wave.seqera.io/library/python:3.12.2--0d47e6fe32e00784' } } +process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } +process { withName: 'CUSTOM_TX2GENE' { container = 'community.wave.seqera.io/library/python:3.10.4--d0dc5eb8ea72fa82' } } +process { withName: 'DESEQ2_QC' { container = 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:8bd3e9db55b129d7' } } +process { withName: 'DUPRADAR' { container = 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--f75495d6abf45328' } } +process { withName: 'FASTP' { container = 'community.wave.seqera.io/library/fastp:0.23.4--c1051f83dcae53f5' } } +process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a' } } +process { withName: 'FQ_LINT' { container = 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } } +process { withName: 'FQ_SUBSAMPLE' { container = 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } } +process { withName: 'GFFREAD' { container = 'community.wave.seqera.io/library/gffread:0.12.7--1577aa7c95340d9f' } } +process { withName: 'GTF2BED' { container = 'community.wave.seqera.io/library/perl:5.26.2--2a6adf51d600e047' } } +process { withName: 'GTF_FILTER' { container = 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } } +process { withName: 'GUNZIP' { container = 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } } +process { withName: 'HISAT2_ALIGN' { container = 'community.wave.seqera.io/library/hisat2_samtools:16f4ce5d5c83f6ec' } } +process { withName: 'HISAT2_BUILD' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--722945b3f185af3d' } } +process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--722945b3f185af3d' } } +process { withName: 'KALLISTO_INDEX' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } } +process { withName: 'KALLISTO_QUANT' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } } +process { withName: 'KRAKEN2_KRAKEN2' { container = 'community.wave.seqera.io/library/kraken2_coreutils_pigz:efede2ece83f7a32' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.27--7cf5785022026d98' } } +process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } } +process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera.io/library/picard:3.1.1--c28da730a329ab3c' } } +process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } } +process { withName: 'PRESEQ_LCEXTRAP' { container = 'community.wave.seqera.io/library/preseq:3.2.0--80c9d2ffee38d3ac' } } +process { withName: 'QUALIMAP_RNASEQ' { container = 'community.wave.seqera.io/library/qualimap:2.3--8375b60bba97a2a6' } } +process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'community.wave.seqera.io/library/rsem_star:871666abaeb8fb01' } } +process { withName: 'RSEM_MERGE_COUNTS' { container = 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } } +process { withName: 'RSEM_PREPAREREFERENCE' { container = 'community.wave.seqera.io/library/rsem_star:871666abaeb8fb01' } } +process { withName: 'RSEQC_BAMSTAT' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'RSEQC_INNERDISTANCE' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'RSEQC_READDISTRIBUTION' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'RSEQC_READDUPLICATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'RSEQC_TIN' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'SALMON_INDEX' { container = 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } } +process { withName: 'SALMON_QUANT' { container = 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } } +process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } +process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } +process { withName: 'SAMTOOLS_INDEX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } +process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } +process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } +process { withName: 'SORTMERNA' { container = 'community.wave.seqera.io/library/sortmerna:4.3.7--4cc83a7bffbaaa61' } } +process { withName: 'STAR_ALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5' } } +process { withName: 'STAR_ALIGN_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:6ae64d775f2cb855' } } +process { withName: 'STAR_GENOMEGENERATE' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5' } } +process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:6ae64d775f2cb855' } } +process { withName: 'STRINGTIE_STRINGTIE' { container = 'community.wave.seqera.io/library/stringtie:2.2.3--77d8df3265c94ba1' } } +process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'community.wave.seqera.io/library/subread:2.0.6--df9c6b502b57bb9c' } } +process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--859858039875a2a5' } } +process { withName: 'TRIMGALORE' { container = 'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:d0b730b6770575ef' } } +process { withName: 'TXIMETA_TXIMPORT' { container = 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--3b0ca8a1710e2b2b' } } +process { withName: 'UCSC_BEDCLIP' { container = 'community.wave.seqera.io/library/ucsc-bedclip:377--489576e83f1992e0' } } +process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--1db18e1b19f8e5f1' } } +process { withName: 'UMICOLLAPSE' { container = 'community.wave.seqera.io/library/umicollapse:1.1.0--d406900dbf84ec60' } } +process { withName: 'UMITOOLS_DEDUP' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } } +process { withName: 'UMITOOLS_EXTRACT' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } } +process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } } +process { withName: 'UNTAR' { container = 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } } diff --git a/conf/containers/containers_singularity_arm64.config b/conf/containers/containers_singularity_arm64.config index 5c5b57da7..5fc385fc5 100644 --- a/conf/containers/containers_singularity_arm64.config +++ b/conf/containers/containers_singularity_arm64.config @@ -1,64 +1,64 @@ -process { withName: 'BBMAP_BBSPLIT' { container = 'docker://community.wave.seqera.io/library/bbmap:39.10--168578230ff6490a' } } -process { withName: 'BEDTOOLS_GENOMECOV' { container = 'docker://community.wave.seqera.io/library/bedtools:2.31.1--7c4ce4cb07c09ee4' } } -process { withName: 'BRACKEN_BRACKEN' { container = 'docker://community.wave.seqera.io/library/bracken:2.9--3d5af74ed6966fc1' } } -process { withName: 'CAT_FASTQ' { container = 'docker://community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' } } -process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'docker://community.wave.seqera.io/library/python:3.12.2--8aba3d9ac529ff19' } } -process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'CUSTOM_TX2GENE' { container = 'docker://community.wave.seqera.io/library/python:3.10.4--a643e28963f01eef' } } -process { withName: 'DESEQ2_QC' { container = 'docker://community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:d06fadc02f8422a2' } } -process { withName: 'DUPRADAR' { container = 'docker://community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--dcb3a3be56be6612' } } -process { withName: 'FASTP' { container = 'docker://community.wave.seqera.io/library/fastp:0.23.4--f8cefc1e5f7a782e' } } -process { withName: 'FASTQC' { container = 'docker://community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29' } } -process { withName: 'FQ_LINT' { container = 'docker://community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } -process { withName: 'FQ_SUBSAMPLE' { container = 'docker://community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } } -process { withName: 'GFFREAD' { container = 'docker://community.wave.seqera.io/library/gffread:0.12.7--33b95f1cfcc0e572' } } -process { withName: 'GTF2BED' { container = 'docker://community.wave.seqera.io/library/perl:5.26.2--e6570c5f08d3e12c' } } -process { withName: 'GTF_FILTER' { container = 'docker://community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } -process { withName: 'GUNZIP' { container = 'docker://community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } -process { withName: 'HISAT2_ALIGN' { container = 'docker://community.wave.seqera.io/library/hisat2_samtools:9ef5e68250d2aa60' } } -process { withName: 'HISAT2_BUILD' { container = 'docker://community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } -process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'docker://community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } } -process { withName: 'KALLISTO_INDEX' { container = 'docker://community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } -process { withName: 'KALLISTO_QUANT' { container = 'docker://community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } } -process { withName: 'KRAKEN2_KRAKEN2' { container = 'docker://community.wave.seqera.io/library/kraken2_coreutils_pigz:0892e153c7954635' } } -process { withName: 'MULTIQC' { container = 'docker://community.wave.seqera.io/library/multiqc:1.27--b0d1ffb40dfd9e97' } } -process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'docker://community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } } -process { withName: 'PICARD_MARKDUPLICATES' { container = 'docker://community.wave.seqera.io/library/picard:3.1.1--bae6cd265e6bf3d3' } } -process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'docker://community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } -process { withName: 'PRESEQ_LCEXTRAP' { container = 'docker://community.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613' } } -process { withName: 'QUALIMAP_RNASEQ' { container = 'docker://community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' } } -process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'docker://community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } -process { withName: 'RSEM_MERGE_COUNTS' { container = 'docker://community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } } -process { withName: 'RSEM_PREPAREREFERENCE' { container = 'docker://community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } } -process { withName: 'RSEQC_BAMSTAT' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_INNERDISTANCE' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_READDISTRIBUTION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_READDUPLICATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'RSEQC_TIN' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } } -process { withName: 'SALMON_INDEX' { container = 'docker://community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } -process { withName: 'SALMON_QUANT' { container = 'docker://community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } } -process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'SAMTOOLS_IDXSTATS' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'SAMTOOLS_INDEX' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'SAMTOOLS_SORT' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'SAMTOOLS_STATS' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } } -process { withName: 'SORTMERNA' { container = 'docker://community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' } } -process { withName: 'STAR_ALIGN' { container = 'docker://community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } -process { withName: 'STAR_ALIGN_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } -process { withName: 'STAR_GENOMEGENERATE' { container = 'docker://community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } } -process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } } -process { withName: 'STRINGTIE_STRINGTIE' { container = 'docker://community.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a' } } -process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'docker://community.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e' } } -process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'docker://community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065' } } -process { withName: 'TRIMGALORE' { container = 'docker://community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d' } } -process { withName: 'TXIMETA_TXIMPORT' { container = 'docker://community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--cd025af46d4ef23a' } } -process { withName: 'UCSC_BEDCLIP' { container = 'docker://community.wave.seqera.io/library/ucsc-bedclip:377--41de764ea1c26af4' } } -process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'docker://community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--f66c00635e28f216' } } -process { withName: 'UMICOLLAPSE' { container = 'docker://community.wave.seqera.io/library/umicollapse:1.1.0--74864b350c72f3a0' } } -process { withName: 'UMITOOLS_DEDUP' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } -process { withName: 'UMITOOLS_EXTRACT' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } -process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } } -process { withName: 'UNTAR' { container = 'docker://community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } } +process { withName: 'BBMAP_BBSPLIT' { container = 'docker://community.wave.seqera.io/library/bbmap:39.10--908996c2fb304bec' } } +process { withName: 'BEDTOOLS_GENOMECOV' { container = 'docker://community.wave.seqera.io/library/bedtools:2.31.1--efd79503b8c63422' } } +process { withName: 'BRACKEN_BRACKEN' { container = 'docker://community.wave.seqera.io/library/bracken:2.9--e06b532ae215c74d' } } +process { withName: 'CAT_FASTQ' { container = 'docker://community.wave.seqera.io/library/coreutils:9.5--3931e2d27d9884e5' } } +process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'docker://community.wave.seqera.io/library/python:3.12.2--0d47e6fe32e00784' } } +process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } +process { withName: 'CUSTOM_TX2GENE' { container = 'docker://community.wave.seqera.io/library/python:3.10.4--d0dc5eb8ea72fa82' } } +process { withName: 'DESEQ2_QC' { container = 'docker://community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:8bd3e9db55b129d7' } } +process { withName: 'DUPRADAR' { container = 'docker://community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--f75495d6abf45328' } } +process { withName: 'FASTP' { container = 'docker://community.wave.seqera.io/library/fastp:0.23.4--c1051f83dcae53f5' } } +process { withName: 'FASTQC' { container = 'docker://community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a' } } +process { withName: 'FQ_LINT' { container = 'docker://community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } } +process { withName: 'FQ_SUBSAMPLE' { container = 'docker://community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } } +process { withName: 'GFFREAD' { container = 'docker://community.wave.seqera.io/library/gffread:0.12.7--1577aa7c95340d9f' } } +process { withName: 'GTF2BED' { container = 'docker://community.wave.seqera.io/library/perl:5.26.2--2a6adf51d600e047' } } +process { withName: 'GTF_FILTER' { container = 'docker://community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } } +process { withName: 'GUNZIP' { container = 'docker://community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } } +process { withName: 'HISAT2_ALIGN' { container = 'docker://community.wave.seqera.io/library/hisat2_samtools:16f4ce5d5c83f6ec' } } +process { withName: 'HISAT2_BUILD' { container = 'docker://community.wave.seqera.io/library/hisat2:2.2.1--722945b3f185af3d' } } +process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'docker://community.wave.seqera.io/library/hisat2:2.2.1--722945b3f185af3d' } } +process { withName: 'KALLISTO_INDEX' { container = 'docker://community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } } +process { withName: 'KALLISTO_QUANT' { container = 'docker://community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } } +process { withName: 'KRAKEN2_KRAKEN2' { container = 'docker://community.wave.seqera.io/library/kraken2_coreutils_pigz:efede2ece83f7a32' } } +process { withName: 'MULTIQC' { container = 'docker://community.wave.seqera.io/library/multiqc:1.27--7cf5785022026d98' } } +process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'docker://community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } } +process { withName: 'PICARD_MARKDUPLICATES' { container = 'docker://community.wave.seqera.io/library/picard:3.1.1--c28da730a329ab3c' } } +process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'docker://community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } } +process { withName: 'PRESEQ_LCEXTRAP' { container = 'docker://community.wave.seqera.io/library/preseq:3.2.0--80c9d2ffee38d3ac' } } +process { withName: 'QUALIMAP_RNASEQ' { container = 'docker://community.wave.seqera.io/library/qualimap:2.3--8375b60bba97a2a6' } } +process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'docker://community.wave.seqera.io/library/rsem_star:871666abaeb8fb01' } } +process { withName: 'RSEM_MERGE_COUNTS' { container = 'docker://community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } } +process { withName: 'RSEM_PREPAREREFERENCE' { container = 'docker://community.wave.seqera.io/library/rsem_star:871666abaeb8fb01' } } +process { withName: 'RSEQC_BAMSTAT' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'RSEQC_INNERDISTANCE' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'RSEQC_READDISTRIBUTION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'RSEQC_READDUPLICATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'RSEQC_TIN' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } +process { withName: 'SALMON_INDEX' { container = 'docker://community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } } +process { withName: 'SALMON_QUANT' { container = 'docker://community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } } +process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } +process { withName: 'SAMTOOLS_IDXSTATS' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } +process { withName: 'SAMTOOLS_INDEX' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } +process { withName: 'SAMTOOLS_SORT' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } +process { withName: 'SAMTOOLS_STATS' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } +process { withName: 'SORTMERNA' { container = 'docker://community.wave.seqera.io/library/sortmerna:4.3.7--4cc83a7bffbaaa61' } } +process { withName: 'STAR_ALIGN' { container = 'docker://community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5' } } +process { withName: 'STAR_ALIGN_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:6ae64d775f2cb855' } } +process { withName: 'STAR_GENOMEGENERATE' { container = 'docker://community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5' } } +process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:6ae64d775f2cb855' } } +process { withName: 'STRINGTIE_STRINGTIE' { container = 'docker://community.wave.seqera.io/library/stringtie:2.2.3--77d8df3265c94ba1' } } +process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'docker://community.wave.seqera.io/library/subread:2.0.6--df9c6b502b57bb9c' } } +process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'docker://community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--859858039875a2a5' } } +process { withName: 'TRIMGALORE' { container = 'docker://community.wave.seqera.io/library/cutadapt_trim-galore_pigz:d0b730b6770575ef' } } +process { withName: 'TXIMETA_TXIMPORT' { container = 'docker://community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--3b0ca8a1710e2b2b' } } +process { withName: 'UCSC_BEDCLIP' { container = 'docker://community.wave.seqera.io/library/ucsc-bedclip:377--489576e83f1992e0' } } +process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'docker://community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--1db18e1b19f8e5f1' } } +process { withName: 'UMICOLLAPSE' { container = 'docker://community.wave.seqera.io/library/umicollapse:1.1.0--d406900dbf84ec60' } } +process { withName: 'UMITOOLS_DEDUP' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } } +process { withName: 'UMITOOLS_EXTRACT' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } } +process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } } +process { withName: 'UNTAR' { container = 'docker://community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } } diff --git a/nextflow.config b/nextflow.config index f58243326..32101af04 100644 --- a/nextflow.config +++ b/nextflow.config @@ -182,7 +182,8 @@ profiles { apptainer.enabled = false } docker { - includeConfig 'conf/containers/containers_docker_amd64.config' + // TODO: https://github.com/nf-core/rnaseq/pull/1515#pullrequestreview-3201429623 + // includeConfig 'conf/containers/containers_docker_amd64.config' docker.enabled = true conda.enabled = false singularity.enabled = false @@ -192,13 +193,13 @@ profiles { apptainer.enabled = false docker.runOptions = '-u $(id -u):$(id -g)' } - arm { - // TODO: Handle docker_arm, singularity_arm, etc. - includeConfig 'conf/containers/containers_docker_arm64.config' + apple { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } + arm { + process.arch = 'linux/arm64' + } singularity { - includeConfig 'conf/containers/containers_singularity_amd64.config' singularity.enabled = true singularity.autoMounts = true conda.enabled = false From 2b678b1d786d20cd298639228394a3a9dee566c4 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 16 Sep 2025 12:50:57 -0500 Subject: [PATCH 15/15] ci: optimize container config workflow MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Update to Nextflow stable version 25.04.7 - Strip back to docker builds only (singularity disabled temporarily) - Update ARM profile from 'arm' to 'arm64' following nf-core standards - Add path filter to run only on modules.json changes 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- .github/workflows/containers_config.yml | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/.github/workflows/containers_config.yml b/.github/workflows/containers_config.yml index e179c3b38..034e96fe6 100644 --- a/.github/workflows/containers_config.yml +++ b/.github/workflows/containers_config.yml @@ -1,11 +1,12 @@ name: Container Configs on: - # FIXME Remove these and only run on release or PRs to main or TEMPLATE updates push: - branches: [main,dev] + branches: [main, dev] + paths: ['modules.json'] pull_request: - branches: [main,dev] + branches: [main, dev] + paths: ['modules.json'] release: types: [published] # TODO workflow_dispatch: @@ -22,14 +23,16 @@ jobs: ref: ${{ github.head_ref }} - uses: nf-core/setup-nextflow@v2 with: - version: "25.01.0-edge" + version: "25.04.7" - name: Snapshot containers run: | mkdir -p conf/containers - for container in docker singularity; do + # TODO: Re-enable singularity builds once singularity image issues are resolved + # https://github.com/nf-core/rnaseq/pull/1515#pullrequestreview-3201429623 + for container in docker; do # singularity for arch in amd64 arm64; do if [ "$arch" = "arm64" ]; then - profile="wave,$container,arm" + profile="wave,$container,arm64" else profile="wave,$container" fi @@ -48,4 +51,3 @@ jobs: git status git commit -m "[automated] Update container configs" git push -