Merge pull request #67 from danilodileo/modules_update

Modules update
nf-core · Jul 24, 2024 · b1392cb · b1392cb
2 parents 4be9105 + 80258a3
commit b1392cb
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Showing 62 changed files with 3,495 additions and 587 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -81,10 +81,6 @@ process {
         ext.args = '--threshold-bp "50"'
     }
 
-    withName: 'SOURMASH_INDEX' {
-        ext.args = "--ksize ${params.ksize}"
-    }
-
     withName: 'GINDEX_CAT' {
         publishDir = [
             path: { "${params.outdir}/concatenate" },
@@ -110,6 +106,17 @@ process {
         ]
     }
 
+    withName: BBMAP_INDEX {
+        publishDir = [
+            [
+                path: { "${params.outdir}/bbmap/" },
+                mode: 'copy',
+                pattern: "*",
+                enabled: params.save_bbmap_index
+            ]
+        ]
+    }
+
     withName: SAMTOOLS_SORT {
         ext.prefix = { "${meta.id}.sorted" }
     }

diff --git a/modules.json b/modules.json
@@ -27,12 +27,12 @@
                     },
                     "cat/cat": {
                         "branch": "master",
-                        "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8",
+                        "git_sha": "5bb8ca085e17549e185e1823495ab8d20727a805",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e",
+                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
                         "installed_by": ["modules"]
                     },
                     "checkm/lineagewf": {
@@ -52,7 +52,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
                     "gtdbtk/classifywf": {
@@ -62,12 +62,12 @@
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "8f2062e7b4185590fb9f43c275381a31a6544fc0",
+                        "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
                         "installed_by": ["modules"]
                     },
                     "prokka": {
@@ -77,27 +77,27 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "sourmash/gather": {
@@ -107,7 +107,7 @@
                     },
                     "sourmash/index": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "1c1bd04e617b2b6b50c48cb7c3f2fba039903a83",
                         "installed_by": ["modules"]
                     },
                     "sourmash/sketch": {
@@ -117,17 +117,17 @@
                     },
                     "subread/featurecounts": {
                         "branch": "master",
-                        "git_sha": "e5265c217dcfbff7731c40623aaf07538fdd3e1c",
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
                         "installed_by": ["modules"]
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "a98418419ae6c9df3cf6cf108d1e1aba71037d5a",
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     }
                 }
@@ -136,12 +136,12 @@
                 "nf-core": {
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
                         "installed_by": ["bam_sort_stats_samtools", "subworkflows"]
                     },
                     "utils_nextflow_pipeline": {

diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf
diff --git a/modules/nf-core/cat/cat/tests/main.nf.test b/modules/nf-core/cat/cat/tests/main.nf.test
diff --git a/modules/nf-core/cat/cat/tests/main.nf.test.snap b/modules/nf-core/cat/cat/tests/main.nf.test.snap
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf