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Merge pull request #142 from nf-cmgg/chore/bump_modules
Chore/bump modules
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‎.github/workflows/template-version-comment.yml‎

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‎.nf-core.yml‎

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@@ -38,5 +38,5 @@ template:
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name: preprocessing
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org: nf-cmgg
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outdir: .
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skip_features: []
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skip_features: ["fastqc"]
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version: 2.1.0dev

‎README.md‎

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@@ -23,7 +23,7 @@ Steps inlcude:
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1. Demultiplexing using [`BCLconvert`](https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html)
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2. Read QC and trimming using [`fastp`](https://github.com/OpenGene/fastp)
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3. Alignment using either [`bwa`](https://github.com/lh3/bwa), [`bwa-mem2`](https://github.com/bwa-mem2/bwa-mem2), [`bowtie2`](https://github.com/BenLangmead/bowtie2), [`dragmap`](https://github.com/Illumina/DRAGMAP) or [`snap`](https://github.com/amplab/snap) for DNA-seq and [`STAR`](https://github.com/alexdobin/STAR) for RNA-seq
26+
3. Alignment using either [`bwa`](https://github.com/lh3/bwa), [`bwa-mem2`](https://github.com/bwa-mem2/bwa-mem2), [`bowtie2`](https://github.com/BenLangmead/bowtie2), [`dragmap`](https://github.com/Illumina/DRAGMAP), [`snap`](https://github.com/amplab/snap) or [`strobe`](https://github.com/ksahlin/strobealign) for DNA-seq and [`STAR`](https://github.com/alexdobin/STAR) for RNA-seq
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4. Duplicate marking using [`bamsormadup`](https://gitlab.com/german.tischler/biobambam2) or [`samtools markdup`](http://www.htslib.org/doc/samtools-markdup.html)
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5. Coverage analysis using [`mosdepth`](https://github.com/brentp/mosdepth) and [`samtools coverage`](http://www.htslib.org/doc/samtools-coverage.html)
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6. Alignment QC using [`samtools flagstat`](http://www.htslib.org/doc/samtools-flagstat.html), [`samtools stats`](http://www.htslib.org/doc/samtools-stats.html), [`samtools idxstats`](http://www.htslib.org/doc/samtools-idxstats.html) and [`picard CollecHsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectHsMetrics), [`picard CollectWgsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectWgsMetrics), [`picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectMultipleMetrics)

‎assets/schema_input.json‎

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"meta": ["aligner"],
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"type": "string",
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"description": "Aligner to use to align sample to the reference genome",
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"enum": ["bowtie2", "bwamem", "bwamem2", "dragmap", "snap", "star"]
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"enum": ["bowtie2", "bwamem", "bwamem2", "dragmap", "snap", "strobe", "star"]
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},
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"tag": {
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"meta": ["tag"],

‎assets/schema_sampleinfo.json‎

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"meta": ["aligner"],
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"type": "string",
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"description": "Aligner to use to align sample to the reference genome",
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"enum": ["bowtie2", "bwamem", "bwamem2", "dragmap", "snap", "star"]
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"enum": ["bowtie2", "bwamem", "bwamem2", "dragmap", "snap", "strobe", "star"]
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}
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}
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},

‎conf/modules.config‎

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@@ -21,7 +21,7 @@ process {
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[
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meta.lane ? "--bcl-only-lane ${meta.lane}" : "",
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"--force",
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"--strict",
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"--strict-mode true",
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].join(" ").trim()
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}
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}
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ext.args = {
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[
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meta.readgroup ? "--rg-line \"@RG\t" + meta.readgroup.findResults { rg -> rg.value?.trim() ? "${rg.key}:${rg.value}" : null }.join("\t") + "\"" : "",
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"--output-fmt cram",
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"--output-fmt cram,version=3.0",
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"--output-fmt-option archive",
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].join(" ").trim()
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}
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// -xf 2 : expansion factor for reading compressed data
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//// SNAP
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withName: SNAP_ALIGN {
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withName: SNAPALIGNER_ALIGN {
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ext.args = {
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[
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"-b-",
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"-d 2500",
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params.umi_aware ? "--barcode-name" : "",
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"--write-index",
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"--output-fmt cram",
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"--output-fmt cram,version=3.0",
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"--output-fmt-option archive",
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].join(" ").trim()
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}
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ext.args = {
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[
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"--write-index",
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"--output-fmt cram",
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"--output-fmt cram,version=3.0",
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"--output-fmt-option archive",
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].join(" ").trim()
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}
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ext.args = {
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[
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"-C",
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"--output-fmt cram",
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"--output-fmt cram,version=3.0",
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"--output-fmt-option archive",
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].join(" ").trim()
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}

‎conf/profiles/s3_ugent.config‎

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aws {
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profile = "ugent"
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client {
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endpoint = "https://s3.ugent.be"
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protocol = "https"

‎main.nf‎

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publish:
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demultiplex_interop = PREPROCESSING.out.demultiplex_interop.transpose(by:1)
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demultiplex_reports = PREPROCESSING.out.demultiplex_reports.map { meta, reports -> [ meta, files("${reports.toUri()}/*") ] }.transpose(by:1)
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demultiplex_logs = PREPROCESSING.out.demultiplex_logs.map { meta, logs -> [ meta, files("${logs.toUri()}/*") ] }.transpose(by:1)
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demultiplex_reports = PREPROCESSING.out.demultiplex_reports.transpose(by:1)
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demultiplex_logs = PREPROCESSING.out.demultiplex_logs.transpose(by:1)
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fastp_json = PREPROCESSING.out.fastp_json
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fastp_html = PREPROCESSING.out.fastp_html
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ucrams = PREPROCESSING.out.ucrams
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bin >> "Interop/${bin.name}"
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} }
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demultiplex_reports { path { meta, report ->
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def out_path = meta.lane ? "Reports/LOO${meta.lane}/${report.name}" as String : "Reports/${report.name}"
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def out_path = meta.lane ? "Reports/L00${meta.lane}/${report.name}" as String : "Reports/${report.name}"
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report >> out_path
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} }
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demultiplex_logs { path { meta, log ->
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def out_path = meta.lane ? "Logs/LOO${meta.lane}/${log.name}" as String : "Logs/${log.name}"
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def out_path = meta.lane ? "Logs/L00${meta.lane}/${log.name}" as String : "Logs/${log.name}"
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log >> out_path
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} }
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fastp_json { path { meta, json ->

‎modules.json‎

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"nf-core": {
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"bcl2fastq": {
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"branch": "master",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"installed_by": ["bcl_demultiplex"]
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},
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"bclconvert": {
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"branch": "master",
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"git_sha": "27cceb2eb8aa959d4a8819caab886386a59a3789",
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"installed_by": ["bcl_demultiplex", "modules"]
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["bcl_demultiplex", "modules"],
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"patch": "modules/nf-core/bclconvert/bclconvert.diff"
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},
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"biobambam/bamsormadup": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/biobambam/bamsormadup/biobambam-bamsormadup.diff"
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},
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"bowtie2/align": {
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"branch": "master",
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"git_sha": "8864afe586537bf562eac7b83349c26207f3cb4d",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["fastq_align_dna", "modules"],
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"patch": "modules/nf-core/bowtie2/align/bowtie2-align.diff"
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},
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"bwa/mem": {
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"branch": "master",
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"git_sha": "a29f18660f5e3748d44d6f716241e70c942c065d",
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"git_sha": "1c46359c837ef768b004519f535c30378e8289fc",
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"installed_by": ["fastq_align_dna"],
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"patch": "modules/nf-core/bwa/mem/bwa-mem.diff"
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},
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"bwamem2/mem": {
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"branch": "master",
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"git_sha": "a29f18660f5e3748d44d6f716241e70c942c065d",
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"git_sha": "d86336f3e7ae0d5f76c67b0859409769cfeb2af2",
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"installed_by": ["fastq_align_dna"],
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"patch": "modules/nf-core/bwamem2/mem/bwamem2-mem.diff"
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},
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"dragmap/align": {
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"branch": "master",
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"git_sha": "8864afe586537bf562eac7b83349c26207f3cb4d",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"installed_by": ["fastq_align_dna"],
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"patch": "modules/nf-core/dragmap/align/dragmap-align.diff"
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},
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"fastp": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/fastp/fastp.diff"
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},
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"fastqc": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "d9ec4ef289ad39b8a662a7a12be50409b11df84b",
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"installed_by": ["modules"]
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},
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"md5sum": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["modules"]
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},
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"mosdepth": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/mosdepth/mosdepth.diff"
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "471cf3ca1617271b9b6fea09ea2ebdee78b874de",
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"git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
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"installed_by": ["modules"]
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},
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"picard/collecthsmetrics": {
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"branch": "master",
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"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/picard/collecthsmetrics/picard-collecthsmetrics.diff"
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},
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"picard/collectmultiplemetrics": {
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"branch": "master",
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"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
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"git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/picard/collectmultiplemetrics/picard-collectmultiplemetrics.diff"
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},
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"picard/collectwgsmetrics": {
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"branch": "master",
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"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
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"git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/picard/collectwgsmetrics/picard-collectwgsmetrics.diff"
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},
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"samtools/cat": {
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"branch": "master",
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"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
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"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/samtools/cat/samtools-cat.diff"
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},
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"samtools/convert": {
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"branch": "master",
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"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/samtools/convert/samtools-convert.diff"
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},
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"samtools/coverage": {
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"branch": "master",
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"git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/samtools/coverage/samtools-coverage.diff"
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},
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"samtools/flagstat": {
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"branch": "master",
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"git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
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"git_sha": "e334e12a1e985adc5ffc3fc78a68be1de711de45",
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"installed_by": ["modules"]
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},
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"samtools/idxstats": {
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"branch": "master",
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"git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
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"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
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"installed_by": ["modules"]
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},
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"samtools/import": {
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"branch": "master",
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"git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
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"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
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"installed_by": ["modules"]
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},
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"samtools/sormadup": {
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"branch": "master",
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"git_sha": "38f3b0200093498b70ac2d63a83eac5642e3c873",
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"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/samtools/sormadup/samtools-sormadup.diff"
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},
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"samtools/sort": {
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"branch": "master",
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"git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
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"git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/samtools/sort/samtools-sort.diff"
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},
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"samtools/stats": {
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"branch": "master",
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"git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
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"git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/samtools/stats/samtools-stats.diff"
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},
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"snapaligner/align": {
145140
"branch": "master",
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"git_sha": "77bdd7e1047d2abe21ae8d89acc295ea553ecbae",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["fastq_align_dna", "modules"],
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"patch": "modules/nf-core/snapaligner/align/snapaligner-align.diff"
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},
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"git_sha": "ce9e10540a1555145ddd1ddd8b15f7443cbe1449",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/star/align/star-align.diff"
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},
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"strobealign": {
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"branch": "master",
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"git_sha": "d5cc72b63c4e1565cb66e83f0577b04c0bb54d5c",
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"installed_by": ["fastq_align_dna", "modules"],
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"patch": "modules/nf-core/strobealign/strobealign.diff"
155156
}
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}
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},
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"subworkflows": {
159160
"nf-core": {
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"bcl_demultiplex": {
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"branch": "master",
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"git_sha": "1a0770da1cf5c5cd388bf888ba8798bc4d1fba56",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["subworkflows"]
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},
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"fastq_align_dna": {
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"branch": "master",
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"git_sha": "a29f18660f5e3748d44d6f716241e70c942c065d",
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"installed_by": ["subworkflows"],
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"patch": "subworkflows/nf-core/fastq_align_dna/fastq_align_dna.diff"
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"git_sha": "070ddae7fb59384d3d85bf69eb9a1d71ab33ada9",
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"installed_by": ["subworkflows"]
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"utils_nextflow_pipeline": {
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"branch": "master",
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175175
},
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"utils_nfcore_pipeline": {
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"branch": "master",
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"git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
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"git_sha": "df4d1c8cdee98a1bbbed8fc51e82296568e0f9c1",
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"installed_by": ["subworkflows"]
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},
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"utils_nfschema_plugin": {

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