Merge branch 'master' into sylph_profile

nf-core · Jan 16, 2025 · 041ef71 · 041ef71
2 parents bb4bb66 + 070b1ad
commit 041ef71
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diff --git a/modules/nf-core/seqkit/fx2tab/environment.yml b/modules/nf-core/seqkit/fx2tab/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.8.1
+  - bioconda::seqkit=2.9.0
diff --git a/modules/nf-core/seqkit/fx2tab/main.nf b/modules/nf-core/seqkit/fx2tab/main.nf
@@ -4,8 +4,8 @@ process SEQKIT_FX2TAB {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0' :
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' :
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fastx)
@@ -34,4 +34,16 @@ process SEQKIT_FX2TAB {
         seqkit: \$( seqkit | sed '3!d; s/Version: //' )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.suffix ?: "txt.zst"
+    """
+    touch ${prefix}.${suffix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: \$( seqkit | sed '3!d; s/Version: //' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/seqkit/fx2tab/tests/main.nf.test.snap b/modules/nf-core/seqkit/fx2tab/tests/main.nf.test.snap
@@ -7,30 +7,30 @@
                         {
                             "id": "test"
                         },
-                        "test.txt.zst:md5,08902131ebe68052a97178bc426bf944"
+                        "test.txt.zst:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,ba37c06c2d66e54301b2cd35ae47d0e8"
+                    "versions.yml:md5,b35c25f76ae716eb6bed4f18abf12d50"
                 ],
                 "text": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.txt.zst:md5,08902131ebe68052a97178bc426bf944"
+                        "test.txt.zst:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ba37c06c2d66e54301b2cd35ae47d0e8"
+                    "versions.yml:md5,b35c25f76ae716eb6bed4f18abf12d50"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-07T16:01:39.484590737"
+        "timestamp": "2025-01-15T12:18:24.281141"
     },
     "sarscov2 - fasta": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,ba37c06c2d66e54301b2cd35ae47d0e8"
+                    "versions.yml:md5,b35c25f76ae716eb6bed4f18abf12d50"
                 ],
                 "text": [
                     [
@@ -55,15 +55,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ba37c06c2d66e54301b2cd35ae47d0e8"
+                    "versions.yml:md5,b35c25f76ae716eb6bed4f18abf12d50"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-07T16:01:21.332957847"
+        "timestamp": "2025-01-15T12:18:14.007765"
     },
     "sarscov2 - fastq": {
         "content": [
@@ -77,7 +77,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,ba37c06c2d66e54301b2cd35ae47d0e8"
+                    "versions.yml:md5,b35c25f76ae716eb6bed4f18abf12d50"
                 ],
                 "text": [
                     [
@@ -88,14 +88,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ba37c06c2d66e54301b2cd35ae47d0e8"
+                    "versions.yml:md5,b35c25f76ae716eb6bed4f18abf12d50"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-07T16:01:29.885155029"
+        "timestamp": "2025-01-15T12:18:19.228692"
     }
 }
diff --git a/modules/nf-core/seqkit/tab2fx/environment.yml b/modules/nf-core/seqkit/tab2fx/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.8.1
+  - bioconda::seqkit=2.9.0
diff --git a/modules/nf-core/seqkit/tab2fx/main.nf b/modules/nf-core/seqkit/tab2fx/main.nf
@@ -4,8 +4,8 @@ process SEQKIT_TAB2FX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0' :
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' :
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(text)
@@ -34,4 +34,16 @@ process SEQKIT_TAB2FX {
         seqkit: \$( seqkit | sed '3!d; s/Version: //' )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.suffix ?: "fa.zst"
+    """
+    touch ${prefix}.${suffix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: \$( seqkit | sed '3!d; s/Version: //' )
+    END_VERSIONS
+    """    
 }
diff --git a/modules/nf-core/seqkit/tab2fx/tests/main.nf.test.snap b/modules/nf-core/seqkit/tab2fx/tests/main.nf.test.snap
@@ -7,30 +7,30 @@
                         {
                             "id": "test"
                         },
-                        "test.fa.zst:md5,04d45a85c10933605cb5a289552c83a0"
+                        "test.fa.zst:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36"
+                    "versions.yml:md5,d01878090b875a05b111ee8a68405491"
                 ],
                 "fastx": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.fa.zst:md5,04d45a85c10933605cb5a289552c83a0"
+                        "test.fa.zst:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36"
+                    "versions.yml:md5,d01878090b875a05b111ee8a68405491"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:24:24.025365917"
+        "timestamp": "2025-01-15T12:20:30.19388"
     },
     "fastq_gz": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36"
+                    "versions.yml:md5,d01878090b875a05b111ee8a68405491"
                 ],
                 "fastx": [
                     [
@@ -55,15 +55,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36"
+                    "versions.yml:md5,d01878090b875a05b111ee8a68405491"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:24:12.779036251"
+        "timestamp": "2025-01-15T12:20:25.318142"
     },
     "fasta_gz": {
         "content": [
@@ -77,7 +77,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36"
+                    "versions.yml:md5,d01878090b875a05b111ee8a68405491"
                 ],
                 "fastx": [
                     [
@@ -88,15 +88,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36"
+                    "versions.yml:md5,d01878090b875a05b111ee8a68405491"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:24:00.497912668"
+        "timestamp": "2025-01-15T12:20:19.111781"
     },
     "fasta": {
         "content": [
@@ -110,7 +110,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36"
+                    "versions.yml:md5,d01878090b875a05b111ee8a68405491"
                 ],
                 "fastx": [
                     [
@@ -121,15 +121,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36"
+                    "versions.yml:md5,d01878090b875a05b111ee8a68405491"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:23:31.940090506"
+        "timestamp": "2025-01-15T12:20:06.405339"
     },
     "fastq": {
         "content": [
@@ -143,7 +143,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36"
+                    "versions.yml:md5,d01878090b875a05b111ee8a68405491"
                 ],
                 "fastx": [
                     [
@@ -154,14 +154,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,60fb327ac9a1ed20945fbb049faa7e36"
+                    "versions.yml:md5,d01878090b875a05b111ee8a68405491"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:23:46.059347765"
+        "timestamp": "2025-01-15T12:20:12.813847"
     }
 }
diff --git a/subworkflows/nf-core/abundance_differential_filter/main.nf b/subworkflows/nf-core/abundance_differential_filter/main.nf
@@ -31,15 +31,16 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
 
     // Set up how the channels crossed below will be used to generate channels for processing
     def criteria = multiMapCriteria { meta_input, abundance, analysis_method, fc_threshold, stat_threshold, meta_exp, samplesheet, meta_contrasts, variable, reference, target ->
+        def meta_for_diff = mergeMaps(meta_contrasts, meta_input) + [ 'method': analysis_method ]
+        def meta_input_new = meta_input + [ 'method': analysis_method ]
         samples_and_matrix:
-            meta_map = meta_input + [ 'method': analysis_method ]
-            [meta_map, samplesheet, abundance]
-        contrasts:
-            meta_map = mergeMaps(meta_contrasts, meta_input) + [ 'method': analysis_method ]
-            [ meta_map, variable, reference, target ]
+            [ meta_input_new, samplesheet, abundance ]
+        contrasts_for_diff:
+            [ meta_for_diff, variable, reference, target ]
         filter_params:
-            meta_map = mergeMaps(meta_contrasts, meta_input) + [ 'method': analysis_method ]
-            [meta_map, [ 'fc_threshold': fc_threshold, 'stat_threshold': stat_threshold ]]
+            [ meta_for_diff, [ 'fc_threshold': fc_threshold, 'stat_threshold': stat_threshold ]]
+        contrasts_for_norm:
+            [ meta_input_new, variable, reference, target ]
     }
 
     // For DIFFERENTIAL modules we need to cross the things we're iterating so we
@@ -70,13 +71,13 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
     // LIMMA_NORM directly. It internally runs normalization + DE analysis.
 
     LIMMA_NORM(
-        norm_inputs.contrasts.filter{it[0].method == 'limma'}.first(),
+        norm_inputs.contrasts_for_norm.filter{it[0].method == 'limma'},
         norm_inputs.samples_and_matrix.filter{it[0].method == 'limma'}
     )
 
     LIMMA_DIFFERENTIAL(
-        inputs.contrasts.filter{it[0].method == 'limma'},
-        inputs.samples_and_matrix.filter { it[0].method == 'limma' }
+        inputs.contrasts_for_diff.filter{ it[0].method == 'limma' },
+        inputs.samples_and_matrix.filter{ it[0].method == 'limma' }
     )
 
     // ----------------------------------------------------
@@ -91,14 +92,14 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
     // DESEQ2_NORM directly. It internally runs normalization + DE analysis.
 
     DESEQ2_NORM(
-        norm_inputs.contrasts.filter{it[0].method == 'deseq2'}.first(),
+        norm_inputs.contrasts_for_norm.filter{it[0].method == 'deseq2'},
         norm_inputs.samples_and_matrix.filter{it[0].method == 'deseq2'},
         ch_control_features.first(),
         ch_transcript_lengths.first()
     )
 
     DESEQ2_DIFFERENTIAL(
-        inputs.contrasts.filter{it[0].method == 'deseq2'},
+        inputs.contrasts_for_diff.filter{it[0].method == 'deseq2'},
         inputs.samples_and_matrix.filter{it[0].method == 'deseq2'},
         ch_control_features.first(),
         ch_transcript_lengths.first()
@@ -112,7 +113,7 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
     // not produce a normalized matrix.
 
     PROPR_PROPD(
-        inputs.contrasts.filter{it[0].method == 'propd'},
+        inputs.contrasts_for_diff.filter{it[0].method == 'propd'},
         inputs.samples_and_matrix.filter { it[0].method == 'propd' }
     )
 

diff --git a/subworkflows/nf-core/abundance_differential_filter/meta.yml b/subworkflows/nf-core/abundance_differential_filter/meta.yml
@@ -133,7 +133,7 @@ output:
 authors:
   - "@pinin4fjords"
   - "@bjlang"
-  - "@araiz2001"
+  - "@caraiz2001"
   - "@suzannejin"
 maintainers:
   - "@pinin4fjords"