feat: update hisat2 modules for strict syntax

modules/nf-core/hisat2/align/environment.yml

@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::hisat2=2.2.2
-  - bioconda::samtools=1.23
+  - bioconda::hisat2=2.2.3
+  - bioconda::samtools=1.24

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

@@ -1,11 +1,11 @@
 process HISAT2_ALIGN {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/hisat2_samtools:5a258fe6e30b2c20' :
-        'community.wave.seqera.io/library/hisat2_samtools:6ca0ef72b662d5c8' }"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+?         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/92/92f546b522b78597047a54609eefcf35a014de082df0e500bc2adf64d2733669/data'
+:         'community.wave.seqera.io/library/hisat2_samtools:a0c9b8ccf8116a89' }"
 
     input:
     tuple val(meta), path(reads)
@@ -14,9 +14,9 @@ process HISAT2_ALIGN {
     val save_unaligned
 
     output:
-    tuple val(meta), path("*.bam")                   , emit: bam
-    tuple val(meta), path("*.log")                   , emit: summary
-    tuple val(meta), path("*fastq.gz"), optional:true, emit: fastq
+    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.log"), emit: summary
+    tuple val(meta), path("*fastq.gz"), optional: true, emit: fastq
     tuple val("${task.process}"), val('hisat2'), eval("hisat2 --version | sed -n '1s/.*version //p'"), emit: versions_hisat2, topic: versions
     tuple val("${task.process}"), val('samtools'), eval("samtools --version | sed -n '1s/samtools //p'"), emit: versions_samtools, topic: versions
 
@@ -27,47 +27,40 @@ process HISAT2_ALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    def strandedness = ''
-    if (meta.strandedness == 'forward') {
-        strandedness = meta.single_end ? '--rna-strandness F' : '--rna-strandness FR'
-    } else if (meta.strandedness == 'reverse') {
-        strandedness = meta.single_end ? '--rna-strandness R' : '--rna-strandness RF'
-    }
-    ss = "$splicesites" ? "--known-splicesite-infile $splicesites" : ''
+    def ss = "${splicesites}" ? "--known-splicesite-infile ${splicesites}" : ''
     def rg = args.contains("--rg-id") ? "" : "--rg-id ${prefix} --rg SM:${prefix}"
     if (meta.single_end) {
         def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
         """
         INDEX=`find -L ./ -name "*.1.ht2*" | sed 's/\\.1.ht2.*\$//'`
         hisat2 \\
             -x \$INDEX \\
-            -U $reads \\
-            $strandedness \\
-            $ss \\
+            -U ${reads} \\
+            ${ss} \\
             --summary-file ${prefix}.hisat2.summary.log \\
-            --threads $task.cpus \\
-            $rg \\
-            $unaligned \\
-            $args \\
+            --threads ${task.cpus} \\
+            ${rg} \\
+            ${unaligned} \\
+            ${args} \\
             | samtools view -bS -F 4 -F 256 - > ${prefix}.bam
         """
-    } else {
+    }
+    else {
         def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         """
         INDEX=`find -L ./ -name "*.1.ht2*" | sed 's/\\.1.ht2.*\$//'`
         hisat2 \\
             -x \$INDEX \\
             -1 ${reads[0]} \\
             -2 ${reads[1]} \\
-            $strandedness \\
-            $ss \\
+            ${ss} \\
             --summary-file ${prefix}.hisat2.summary.log \\
-            --threads $task.cpus \\
-            $rg \\
-            $unaligned \\
+            --threads ${task.cpus} \\
+            ${rg} \\
+            ${unaligned} \\
             --no-mixed \\
             --no-discordant \\
-            $args \\
+            ${args} \\
             | samtools view -bS -F 4 -F 8 -F 256 - > ${prefix}.bam
 
         if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
@@ -88,5 +81,4 @@ process HISAT2_ALIGN {
     touch ${prefix}.hisat2.summary.log
     touch ${prefix}.bam
     """
-
 }

modules/nf-core/hisat2/align/meta.yml

@@ -7,9 +7,7 @@ keywords:
   - reference
 tools:
   - hisat2:
-      description: HISAT2 is a fast and sensitive alignment program for mapping next-generation
-        sequencing reads (both DNA and RNA) to a population of human genomes as well
-        as to a single reference genome.
+      description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.
       homepage: https://daehwankimlab.github.io/hisat2/
       documentation: https://daehwankimlab.github.io/hisat2/manual/
       doi: "10.1038/s41587-019-0201-4"
@@ -134,3 +132,27 @@ authors:
 maintainers:
   - "@ntoda03"
   - "@ramprasadn"
+containers:
+  docker:
+    linux/amd64:
+      name: community.wave.seqera.io/library/hisat2_samtools:a0c9b8ccf8116a89
+      build_id: bd-a0c9b8ccf8116a89_1
+      scan_id: sc-886103d0f76f5df6_1
+    linux/arm64:
+      name: community.wave.seqera.io/library/hisat2_samtools:2061bdd7bd29b1cd
+      build_id: bd-2061bdd7bd29b1cd_1
+      scan_id: sc-184bae2a6fa4d5eb_1
+  singularity:
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/hisat2_samtools:c8aaaadb7f843dc5
+      build_id: bd-c8aaaadb7f843dc5_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/92/92f546b522b78597047a54609eefcf35a014de082df0e500bc2adf64d2733669/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/hisat2_samtools:85c43579819c7f9c
+      build_id: bd-85c43579819c7f9c_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0a/0ac773ba54fb01c7ec8666b1347db8c0c5100a8e8b34e5ee5ee3f92abebd8ee7/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/hisat2/align/.conda-lock/linux_amd64-bd-a0c9b8ccf8116a89_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/hisat2/align/.conda-lock/linux_arm64-bd-2061bdd7bd29b1cd_1.txt