replace csvtk/concat module with cat/cat module from nf-core

mskcc · Aug 5, 2023 · bc41e13 · bc41e13
1 parent 8fbdb67
commit bc41e13
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Showing 7 changed files with 109 additions and 106 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -181,7 +181,6 @@ process {
     }
 
     withName: MERGE_CFF {
-        ext.args = {  "-H " }
         publishDir = [
             enabled: false
         ]

diff --git a/modules.json b/modules.json
@@ -10,12 +10,12 @@
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
-                    "cat/fastq": {
+                    "cat/cat": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
-                    "csvtk/concat": {
+                    "cat/fastq": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]

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/meta.yml b/modules/nf-core/cat/cat/meta.yml
diff --git a/modules/nf-core/csvtk/concat/main.nf b/modules/nf-core/csvtk/concat/main.nf
diff --git a/modules/nf-core/csvtk/concat/meta.yml b/modules/nf-core/csvtk/concat/meta.yml
diff --git a/subworkflows/local/fusion.nf b/subworkflows/local/fusion.nf
@@ -4,11 +4,10 @@ include { STAR_ALIGN as STAR_FOR_STARFUSION } from '../../modules/nf-core/star/a
 include { STARFUSION                        } from '../../modules/local/starfusion/detect/main'
 include { FUSIONCATCHER_DETECT              } from '../../modules/local/fusioncatcher/detect/main'
 include { ONCOKB_FUSIONANNOTATOR            } from '../../modules/local/oncokb/fusionannotator/main'
-include { CSVTK_CONCAT as CSV_TO_TSV        } from '../../modules/nf-core/csvtk/concat/main'
 include { TO_CFF as ARRIBA_TO_CFF           } from '../../modules/local/convert_to_cff/main'
 include { TO_CFF as FUSIONCATCHER_TO_CFF    } from '../../modules/local/convert_to_cff/main'
 include { TO_CFF as STARFUSION_TO_CFF       } from '../../modules/local/convert_to_cff/main'
-include { CSVTK_CONCAT as MERGE_CFF         } from '../../modules/nf-core/csvtk/concat/main'
+include { CAT_CAT as MERGE_CFF              } from '../../modules/nf-core/cat/cat/main'
 include { METAFUSION                        } from '../../modules/local/metafusion/main'
 include { ADD_FLAG                          } from '../../modules/local/add_flags/main'
 
@@ -86,20 +85,20 @@ workflow FUSION {
                     .map{ meta, file -> [ meta, "fusioncatcher", file ] } )
     STARFUSION_TO_CFF(STARFUSION.out.abridged
                     .map{ meta, file -> [ meta, "starfusion", file ] })
-    MERGE_CFF(ARRIBA_TO_CFF.out.cff
+    MERGE_CFF(
+        ARRIBA_TO_CFF.out.cff
             .map{ meta, file -> [meta, file]}
             .mix(
                 FUSIONCATCHER_TO_CFF.out.cff
-                .map{ meta, file -> [meta, file]}
+                    .map{ meta, file -> [meta, file]}
             ).mix(
                 STARFUSION_TO_CFF.out.cff
-                .map{ meta, file -> [meta, file]}
+                    .map{ meta, file -> [meta, file]}
             ).groupTuple(by:[0]),
-        'tsv',
-        'tsv')
+    )
 
     METAFUSION(
-        MERGE_CFF.out.csv,
+        MERGE_CFF.out.file_out,
         gene_bed,
         gene_info,
         fasta,