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Update more sentieon modules (#9735)
* Fix environment variable references for strict syntax compliance Wrap environment variables in env() function to comply with Nextflow strict syntax mode (NXF_SYNTAX_PARSER=v2). This addresses 58 lint errors across Sentieon and Spotiflow module test configs. Changes: - Sentieon modules: Replace ${SENTIEON_LICSRVR_IP} with ${env('SENTIEON_LICSRVR_IP')} - Sentieon modules: Replace ${SENTIEON_AUTH_MECH} with ${env('SENTIEON_AUTH_MECH')} - Spotiflow module: Replace ${HOME} with ${env('HOME')} This is part of the migration to Nextflow strict syntax where implicit environment variable references are not allowed. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com> * Use System.getenv() for backwards compatability * Update sentieon/bwamem to topic * Add bwa version back * Fix linting * Swap environment.yml to new version * Use nft-bam * Use nft-bam * Update all sentieon modules * Fix some modules * Prettier * Add missing variable from stub * Update qualcal * Update varcal * More updates * Fix singularity container for wgsmetrics and conda versions * Fix some undefined it warnings * Update snapshot * Remove trailing spaces * Fix wgsmetrics linting * Fix dedup * Fix sentieon/dedup * Update more modules * Update more modules * Bump all modules to 202503.02 * Update snapshots * Update datametrics and rsem * Update rsem * Use correct version * Update datametrics --------- Co-authored-by: Phil Ewels <phil.ewels@seqera.io> Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>
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Lines changed: 705 additions & 714 deletions

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‎modules/nf-core/sentieon/datametrics/environment.yml‎

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@@ -4,5 +4,5 @@ channels:
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- conda-forge
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- bioconda
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dependencies:
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- bioconda::sentieon=202503.01
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- bioconda::sentieon=202503.02
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- conda-forge::gnuplot=5.4.10

‎modules/nf-core/sentieon/datametrics/main.nf‎

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@@ -5,8 +5,8 @@ process SENTIEON_DATAMETRICS {
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/20/2050c5321a5426e31b9ed1e3e98356913fe3c316a7ef02c4fb872983a730db6f/data'
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: 'community.wave.seqera.io/library/sentieon_gnuplot:a6da525a6c9ce6e3'}"
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? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ae/ae67a134620c3af22c8563a2913c4639caa0d75ce25764e7b10c996b242aa023/data'
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: 'community.wave.seqera.io/library/sentieon_gnuplot:41931fca35668c97'}"
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input:
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tuple val(meta), path(bam), path(bai)
@@ -25,7 +25,7 @@ process SENTIEON_DATAMETRICS {
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tuple val(meta), path('*qd_metrics.pdf'), emit: qd_plot, optional: true
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tuple val(meta), path('*is_metrics.pdf'), emit: is_plot, optional: true
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tuple val(meta), path('*gc_metrics.pdf'), emit: gc_plot, optional: true
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path "versions.yml", emit: versions
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tuple val("${task.process}"), val('sentieon'), eval('sentieon driver --version | sed "s/.*-//g"'), topic: versions, emit: versions_sentieon
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when:
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task.ext.when == null || task.ext.when
@@ -59,11 +59,6 @@ process SENTIEON_DATAMETRICS {
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sentieon plot QualDistribution -o ${prefix}_qd_metrics.pdf ${prefix}_qd_metrics.txt
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sentieon plot InsertSizeMetricAlgo -o ${prefix}_is_metrics.pdf ${prefix}_is_metrics.txt
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
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END_VERSIONS
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"""
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stub:
@@ -83,10 +78,5 @@ process SENTIEON_DATAMETRICS {
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touch ${prefix}_qd_metrics.pdf
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touch ${prefix}_is_metrics.pdf
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
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END_VERSIONS
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"""
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}

‎modules/nf-core/sentieon/datametrics/meta.yml‎

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Original file line numberDiff line numberDiff line change
@@ -168,13 +168,27 @@ output:
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description: "PDF containing plot of GC bias"
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pattern: "*.pdf"
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ontologies: []
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versions_sentieon:
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- - ${task.process}:
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type: string
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description: The process the versions were collected from
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- sentieon:
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type: string
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description: The tool name
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- sentieon driver --version | sed "s/.*-//g":
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type: string
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description: The command used to generate the version of the tool
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topics:
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versions:
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- versions.yml:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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ontologies:
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- edam: http://edamontology.org/format_3750 # YAML
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- - ${task.process}:
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type: string
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description: The process the versions were collected from
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- sentieon:
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type: string
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description: The tool name
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- sentieon driver --version | sed "s/.*-//g":
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type: string
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description: The command used to generate the version of the tool
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authors:
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- "@ramprasadn"
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maintainers:

‎modules/nf-core/sentieon/datametrics/tests/main.nf.test‎

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Original file line numberDiff line numberDiff line change
@@ -35,7 +35,16 @@ nextflow_process {
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then {
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assert process.success
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assertAll(
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{ assert snapshot(process.out).match() }
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{ assert snapshot(
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path(process.out.mq_metrics[0][1]).readLines()[1..3].join("\n").md5(),
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path(process.out.qd_metrics[0][1]).readLines()[1..3].join("\n").md5(),
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path(process.out.gc_summary[0][1]).readLines()[1..3].join("\n").md5(),
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path(process.out.gc_metrics[0][1]).readLines()[1..3].join("\n").md5(),
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path(process.out.aln_metrics[0][1]).readLines()[1..3].join("\n").md5(),
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path(process.out.is_metrics[0][1]).readLines()[1..3].join("\n").md5(),
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process.out.findAll { key, val -> key.startsWith("versions") }
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).match()
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}
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)
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}
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}
@@ -66,17 +75,17 @@ nextflow_process {
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assert process.success
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assertAll(
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{ assert snapshot(
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process.out.mq_metrics,
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process.out.qd_metrics,
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process.out.gc_summary,
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process.out.gc_metrics,
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process.out.aln_metrics,
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process.out.is_metrics,
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path(process.out.mq_metrics[0][1]).readLines()[1..3].join("\n").md5(),
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path(process.out.qd_metrics[0][1]).readLines()[1..3].join("\n").md5(),
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path(process.out.gc_summary[0][1]).readLines()[1..3].join("\n").md5(),
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path(process.out.gc_metrics[0][1]).readLines()[1..3].join("\n").md5(),
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path(process.out.aln_metrics[0][1]).readLines()[1..3].join("\n").md5(),
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path(process.out.is_metrics[0][1]).readLines()[1..3].join("\n").md5(),
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file(process.out.mq_plot[0][1]).name,
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file(process.out.qd_plot[0][1]).name,
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file(process.out.is_plot[0][1]).name,
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file(process.out.gc_plot[0][1]).name,
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path(process.out.versions[0]).yaml
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process.out.findAll { key, val -> key.startsWith("versions") }
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).match()
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}
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)

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