Merge branch 'master' into nf-test/mitohifi_findmitoreference

nf-core · Sep 5, 2024 · 7c5505d · 7c5505d
2 parents 5a36a04 + d576f75
commit 7c5505d
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -258,8 +258,6 @@ jobs:
             tags: cellrangerarc/count
           - profile: conda
             tags: cellrangerarc/mkfastq
-          - profile: conda
-            tags: cellrangerarc/mkgtf
           - profile: conda
             tags: cellrangerarc/mkref
           - profile: conda
@@ -318,6 +316,8 @@ jobs:
             tags: islandpath
           - profile: conda
             tags: manta/convertinversion
+          - profile: conda
+            tags: mcstaging/imc2mc
           - profile: conda
             tags: mcquant
           - profile: conda
@@ -470,7 +470,7 @@ jobs:
 
       - name: Upload logs on failure
         if: failure()
-        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4
+        uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4
         with:
           name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
           path: |
@@ -542,6 +542,8 @@ jobs:
             path: modules/nf-core/ensemblvep/vep
           - profile: conda
             path: modules/nf-core/fastk/fastk
+          - profile: conda
+            path: modules/nf-core/cellrangerarc/mkgtf
           - profile: conda
             path: modules/nf-core/fastk/histex
           - profile: conda
@@ -570,8 +572,12 @@ jobs:
             path: modules/nf-core/ilastik/pixelclassification
           - profile: conda
             path: modules/nf-core/imputeme/vcftoprs
+          - profile: conda
+            path: modules/nf-core/mcstaging/imc2mc
           - profile: conda
             path: modules/nf-core/mcquant
+          - profile: conda
+            path: modules/nf-core/mcstaging/phenoimager2mc
           - profile: conda
             path: modules/nf-core/merquryfk/katcomp
           - profile: conda

diff --git a/modules/environment-schema.json b/modules/environment-schema.json
@@ -10,14 +10,9 @@
         },
         "channels": {
             "type": "array",
-            "items": [
-                {
-                    "enum": ["conda-forge"]
-                },
-                {
-                    "enum": ["bioconda"]
-                }
-            ],
+            "items": {
+                "enum": ["bioconda", "conda-forge"]
+            },
             "minItems": 2
         },
         "dependencies": {

diff --git a/modules/nf-core/bcftools/merge/environment.yml b/modules/nf-core/bcftools/merge/environment.yml
@@ -2,6 +2,5 @@ name: bcftools_merge
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bcftools=1.20
diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf
@@ -11,19 +11,20 @@ process BCFTOOLS_MERGE {
     tuple val(meta), path(vcfs), path(tbis)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fai)
-    path(bed)
+    tuple val(meta4), path(bed)
 
     output:
-    tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: merged_variants
+    tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf
+    tuple val(meta), path("*.{csi,tbi}")      , emit: index, optional: true
     path "versions.yml"                       , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args   ?: ''
-    def prefix   = task.ext.prefix ?: "${meta.id}"
-
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def input = vcfs.sort{ it.name }
     def regions = bed ? "--regions-file $bed" : ""
     def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
                     args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
@@ -37,7 +38,7 @@ process BCFTOOLS_MERGE {
         $regions \\
         --threads $task.cpus \\
         --output ${prefix}.${extension} \\
-        $vcfs
+        $input
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -53,8 +54,16 @@ process BCFTOOLS_MERGE {
                     args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
                     args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
                     "vcf"
+    def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
+                args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
+                args.contains("--write-index") || args.contains("-W") ? "csi" :
+                ""
+    def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
+    def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""
+
     """
-    touch ${prefix}.${extension}
+    ${create_cmd} ${prefix}.${extension}
+    ${create_index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/bcftools/merge/meta.yml b/modules/nf-core/bcftools/merge/meta.yml
@@ -46,6 +46,11 @@ input:
       type: file
       description: "(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter)"
       pattern: "*.fai"
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing bed information
+        e.g. [ id:'genome' ]
   - bed:
       type: file
       description: "(Optional) The bed regions to merge on"
@@ -56,22 +61,14 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - vcf_gz:
-      type: file
-      description: VCF merged output file (bgzipped) => when `--output-type z` is used
-      pattern: "*.vcf.gz"
   - vcf:
       type: file
-      description: VCF merged output file => when `--output-type v` is used
-      pattern: "*.vcf"
-  - bcf_gz:
-      type: file
-      description: BCF merged output file (bgzipped) => when `--output-type b` is used
-      pattern: "*.bcf.gz"
-  - bcf:
+      description: merged output file
+      pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+  - index:
       type: file
-      description: BCF merged output file => when `--output-type u` is used
-      pattern: "*.bcf"
+      description: index of merged output
+      pattern: "*.{csi,tbi}"
   - versions:
       type: file
       description: File containing software versions

diff --git a/modules/nf-core/bcftools/merge/tests/bcf.config b/modules/nf-core/bcftools/merge/tests/bcf.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = '--output-type u --no-version'
+}
diff --git a/modules/nf-core/bcftools/merge/tests/bcf_gz.config b/modules/nf-core/bcftools/merge/tests/bcf_gz.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = '--output-type b --no-version'
+}