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Merge pull request #1138 from mahesh-panchal/dev
Update FastQC and UMItools modules
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‎CHANGELOG.md‎

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@@ -10,11 +10,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### Enhancements & fixes
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- [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling.
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- [PR #1138](https://github.com/nf-core/rnaseq/pull/1138) - Updates FASTQC and UMITOOLS modules and their dependencies which have had their version string extraction commands updated ([#1103](https://github.com/nf-core/rnaseq/issues/1103))
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- Update Rseqc and Fastp modules to print STDERR to screen and file.
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### Software dependencies
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| Dependency | Old version | New version |
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| ---------- | ----------- | ----------- |
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| `picard` | 3.0.0 | 3.1.1 |
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| `samtools` | 1.17 | 1.18 |
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> **NB:** Dependency has been **updated** if both old and new version information is present.
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>
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> **NB:** Dependency has been **added** if just the new version information is present.
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>
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> **NB:** Dependency has been **removed** if new version information isn't present.
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### Modules / Subworkflows
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- BAM_RSEQC subworkflow updated with new channel names.
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## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-21
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### Credits

‎modules.json‎

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},
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"fastp": {
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"branch": "master",
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"git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
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"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
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"git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde",
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"installed_by": ["modules", "fastq_fastqc_umitools_fastp"]
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},
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"fastqc": {
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"branch": "master",
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"git_sha": "102cc9b709a6da9f7cee2373563ab1464fca9c0a",
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"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
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"installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"]
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},
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"fq/subsample": {
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},
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"picard/markduplicates": {
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"branch": "master",
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"git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448",
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"git_sha": "20b0918591d4ba20047d7e13e5094bcceba81447",
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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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"rseqc/bamstat": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "65acf692457e8c466e104c6a3e5ac392e98fe688",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/inferexperiment": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "f2a3328fde9a2b4185285057f8d3727f39dd2aef",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/innerdistance": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "3e839096a1be5da4f68d1de1066e4d0bc13f5d6d",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/junctionannotation": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/junctionsaturation": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "9dfed3180f80f599c91daf5112d73a5e59367c24",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/readdistribution": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "7bb1b295a359bcbf0a0ea03d19d40a00916805ee",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/readduplication": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "db02573fdd89210d09ce9e2ac06857902a7fffec",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/tin": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "4acfdd20843d5b6d63f9181721a6856447cb7bec",
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"installed_by": ["bam_rseqc"]
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},
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"salmon/index": {
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},
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"samtools/flagstat": {
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"branch": "master",
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"git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
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"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
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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": "e662ab16e0c11f1e62983e21de9871f59371a639",
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"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
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"installed_by": ["bam_stats_samtools"]
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},
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"samtools/index": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
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"installed_by": [
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"bam_dedup_stats_samtools_umitools",
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"bam_markduplicates_picard",
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"bam_sort_stats_samtools",
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"bam_dedup_stats_samtools_umitools"
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"bam_sort_stats_samtools"
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]
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},
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"samtools/sort": {
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"branch": "master",
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"git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
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"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
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"installed_by": ["bam_sort_stats_samtools"]
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},
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"samtools/stats": {
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"branch": "master",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
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"installed_by": ["bam_stats_samtools"]
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},
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"sortmerna": {
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},
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"trimgalore": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
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"installed_by": ["fastq_fastqc_umitools_trimgalore"]
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},
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"ucsc/bedclip": {
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},
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"umitools/dedup": {
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"branch": "master",
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"git_sha": "7297204bf49273300a3dbfa4b7a4027c8683f1bd",
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"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
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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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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
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"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
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"installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"]
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},
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"untar": {
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"branch": "master",
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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": "dedc0e31087f3306101c38835d051bf49789445a",
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"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
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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": "dedc0e31087f3306101c38835d051bf49789445a",
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"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
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"installed_by": ["subworkflows"]
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},
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"bam_rseqc": {
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"branch": "master",
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"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"git_sha": "92793c143c93acd9129f15f35f25d3aab2b23c0e",
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"installed_by": ["subworkflows"]
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},
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"bam_sort_stats_samtools": {
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"branch": "master",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
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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": "dedc0e31087f3306101c38835d051bf49789445a",
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"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
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"installed_by": [
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"bam_dedup_stats_samtools_umitools",
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"bam_markduplicates_picard",
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"bam_dedup_stats_samtools_umitools"
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"bam_sort_stats_samtools"
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]
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},
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"bedgraph_bedclip_bedgraphtobigwig": {
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},
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"fastq_fastqc_umitools_fastp": {
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"branch": "master",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"git_sha": "3e8b0c1144ccf60b7848efbdc2be285ff20b49ee",
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"installed_by": ["subworkflows"]
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},
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"fastq_fastqc_umitools_trimgalore": {
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"branch": "master",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
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"installed_by": ["subworkflows"]
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},
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"fastq_subsample_fq_salmon": {

‎modules/nf-core/fastp/environment.yml‎

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‎modules/nf-core/fastp/main.nf‎

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‎modules/nf-core/fastp/meta.yml‎

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