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drpatelhdrpatelh
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Run nf-core modules update --all
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‎CHANGELOG.md‎

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@@ -30,9 +30,11 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
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### Software dependencies
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| Dependency | Old version | New version |
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| ---------- | ----------- | ----------- |
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| `fastqc` | 0.11.9 | 0.12.1 |
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| Dependency | Old version | New version |
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| ----------------------- | ----------- | ----------- |
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| `fastqc` | 0.11.9 | 0.12.1 |
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| `multiqc` | 1.14 | 1.15 |
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| `ucsc-bedgraphtobigwig` | 377 | 445 |
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> **NB:** Dependency has been **updated** if both old and new version information is present.
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>

‎docs/usage.md‎

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@@ -91,9 +91,9 @@ The `--umitools_grouping_method` parameter affects [how similar, but non-identic
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#### Examples:
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| UMI type | Source | Pipeline parameters |
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| ------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------- |
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| In read name | [Illumina BCL convert >3.7.5](https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl_convert/bcl-convert-v3-7-5-software-guide-1000000163594-00.pdf) | `--with_umi --skip_umi_extract --umitools_umi_separator ":"` |
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| UMI type | Source | Pipeline parameters |
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| ------------ | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------- |
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| In read name | [Illumina BCL convert >3.7.5](https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl_convert/bcl-convert-v3-7-5-software-guide-1000000163594-00.pdf) | `--with_umi --skip_umi_extract --umitools_umi_separator ":"` |
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| In sequence | [Lexogen QuantSeq® 3’ mRNA-Seq V2 FWD](https://www.lexogen.com/quantseq-3mrna-sequencing) + [UMI Second Strand Synthesis Module](https://faqs.lexogen.com/faq/how-can-i-add-umis-to-my-quantseq-libraries) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{6})(?P<discard_1>.{4}).*"` |
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| In sequence | [Lexogen CORALL® Total RNA-Seq V1](https://www.lexogen.com/corall-total-rna-seq/)<br> > _mind [Appendix H](https://www.lexogen.com/wp-content/uploads/2020/04/095UG190V0130_CORALL-Total-RNA-Seq_2020-03-31.pdf) regarding optional trimming_ | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{12}).*"`<br>Optional: `--clip_r2 9 --three_prime_clip_r2 12` |
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| In sequence | [Takara Bio SMARTer® Stranded Total RNA-Seq Kit v3](https://www.takarabio.com/documents/User%20Manual/SMARTer%20Stranded%20Total%20RNA/SMARTer%20Stranded%20Total%20RNA-Seq%20Kit%20v3%20-%20Pico%20Input%20Mammalian%20User%20Manual-a_114949.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*"` |

‎modules.json‎

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"nf-core": {
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"bbmap/bbsplit": {
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"branch": "master",
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"git_sha": "e228790f2957152ad2534e39abd7b3878963e89d",
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"git_sha": "de3e6fc949dcffb8d3508c015f435ace5773ff08",
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"installed_by": ["modules"]
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},
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"cat/fastq": {
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},
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"custom/dumpsoftwareversions": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "1b372269755a5c4a13c23bc130ebada8cb9d4cd0",
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"installed_by": ["modules"]
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},
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"custom/getchromsizes": {
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
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"git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
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"installed_by": ["modules"]
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},
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"hisat2/align": {
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"branch": "master",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"git_sha": "a1881f6374506f9e031b7af814768cdb44a6a7d3",
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"installed_by": ["fastq_align_hisat2"]
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},
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"hisat2/build": {
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"branch": "master",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"git_sha": "f2f48836bf5c59434966a6c3b2211b29363f31ab",
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"installed_by": ["modules"]
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},
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"hisat2/extractsplicesites": {
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},
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"picard/markduplicates": {
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"branch": "master",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448",
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"installed_by": ["bam_markduplicates_picard"]
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},
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"preseq/lcextrap": {
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},
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"qualimap/rnaseq": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "4657d98bc9f565e067c4d924126ce107056f5e2f",
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"installed_by": ["modules"]
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},
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"rsem/calculateexpression": {
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},
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"salmon/quant": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "c5b528d0a51c31621b485ab3bcc008f483619ea6",
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"installed_by": ["modules", "fastq_subsample_fq_salmon"]
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},
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"samtools/flagstat": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
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"installed_by": ["bam_stats_samtools"]
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},
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"samtools/idxstats": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
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"installed_by": ["bam_stats_samtools"]
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},
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"samtools/index": {
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},
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"star/align": {
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"branch": "master",
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"git_sha": "57d75dbac06812c59798a48585032f6e50bb1914",
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"git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
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"installed_by": ["modules"]
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},
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"star/genomegenerate": {
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"branch": "master",
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"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
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"git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
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"installed_by": ["modules"]
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},
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"stringtie/stringtie": {
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},
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"ucsc/bedclip": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "240937a2a9c30298110753292be041188891f2cb",
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"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
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},
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"ucsc/bedgraphtobigwig": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "66290981ab6038ea86177ade40b9449bc790b0ce",
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"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
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},
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"umitools/dedup": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "7297204bf49273300a3dbfa4b7a4027c8683f1bd",
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"installed_by": ["bam_dedup_stats_samtools_umitools"]
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},
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"umitools/extract": {
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"nf-core": {
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"bam_dedup_stats_samtools_umitools": {
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"branch": "master",
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"git_sha": "e228790f2957152ad2534e39abd7b3878963e89d",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": ["subworkflows"]
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},
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"bam_markduplicates_picard": {
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"branch": "master",
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"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": ["subworkflows"]
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},
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"bam_rseqc": {
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},
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"bam_sort_stats_samtools": {
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"branch": "master",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": ["fastq_align_hisat2"]
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},
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"bam_stats_samtools": {
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"branch": "master",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": [
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"bam_markduplicates_picard",
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"bam_sort_stats_samtools",
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"bam_markduplicates_picard",
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"bam_dedup_stats_samtools_umitools"
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]
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},
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"bedgraph_bedclip_bedgraphtobigwig": {
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"branch": "master",
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"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": ["subworkflows"]
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},
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"fastq_align_hisat2": {
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"branch": "master",
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"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": ["subworkflows"]
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},
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"fastq_fastqc_umitools_fastp": {
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},
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"fastq_subsample_fq_salmon": {
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"branch": "master",
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"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": ["subworkflows"]
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}
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}

‎modules/nf-core/bbmap/bbsplit/main.nf‎

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‎modules/nf-core/custom/dumpsoftwareversions/main.nf‎

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‎modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test‎

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‎modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap‎

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‎modules/nf-core/gunzip/main.nf‎

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‎modules/nf-core/hisat2/align/main.nf‎

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‎modules/nf-core/hisat2/build/main.nf‎

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