nf-core · maxulysse · Nov 19, 2025 · Oct 1, 2025 · Oct 2, 2025 · Oct 2, 2025
diff --git a/conf/modules.config b/conf/modules.config
@@ -49,6 +49,29 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+    withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
+        publishDir = [
+            path: { "${params.outdir}/picard_collectmultiplemetrics" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'SAMTOOLS_FAIDX' {
+        publishDir = [
+            path: { "${params.outdir}/samtools_faidx" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'SAMTOOLS_INDEX' {
+        publishDir = [
+            path: { "${params.outdir}/bwamem2_mem" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }

diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "bowtie2/build": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
@@ -17,7 +17,7 @@
                     },
                     "bwamem2/mem": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "d86336f3e7ae0d5f76c67b0859409769cfeb2af2",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/bwamem2/mem/bwamem2-mem.diff"
                     },
@@ -28,18 +28,18 @@
                     },
                     "fastqscreen/buildfromindex": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff"
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
+                        "git_sha": "82a79183037a403ad1b6714e5dbcff25500efaf6",
                         "installed_by": ["modules"]
                     },
                     "picard/collectmultiplemetrics": {
@@ -49,7 +49,7 @@
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
@@ -59,12 +59,12 @@
                     },
                     "seqfu/stats": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "seqtk/sample": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/nf-core/bowtie2/build/environment.yml b/modules/nf-core/bowtie2/build/environment.yml
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
diff --git a/modules/nf-core/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml
diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test b/modules/nf-core/bowtie2/build/tests/main.nf.test
diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test.snap b/modules/nf-core/bowtie2/build/tests/main.nf.test.snap
diff --git a/modules/nf-core/bowtie2/build/tests/tags.yml b/modules/nf-core/bowtie2/build/tests/tags.yml
diff --git a/modules/nf-core/bwamem2/mem/bwamem2-mem.diff b/modules/nf-core/bwamem2/mem/bwamem2-mem.diff
diff --git a/modules/nf-core/bwamem2/mem/environment.yml b/modules/nf-core/bwamem2/mem/environment.yml
diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap
diff --git a/modules/nf-core/fastqscreen/buildfromindex/environment.yml b/modules/nf-core/fastqscreen/buildfromindex/environment.yml
diff --git a/modules/nf-core/fastqscreen/buildfromindex/meta.yml b/modules/nf-core/fastqscreen/buildfromindex/meta.yml