Replace nfcore modules

.github/workflows/linting.yml

@@ -120,7 +120,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core git+https://github.com/nf-core/tools.git@dev
+          pip install nf-core
 
       - name: Run nf-core lint
         env:

conf/modules.config

@@ -167,7 +167,7 @@ if (('markduplicates' in params.use_gatk_spark) && (!params.skip_markduplicates)
 // MARKDUPLICATES
 process {
     withName: 'GATK4_ESTIMATELIBRARYCOMPLEXITY' {
-        ext.suffix       = '.md'
+        ext.prefix       = {"${meta.id}.md"}
         publishDir       = [
             path: { "${params.outdir}/preprocessing/${meta.id}/markduplicates" },
             enabled: true,
@@ -176,7 +176,7 @@ process {
     }
     withName: 'GATK4_MARKDUPLICATES' {
         ext.args         = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT'
-        ext.suffix       = '.md'
+        ext.prefix       = {"${meta.id}.md"}
         publishDir       = [
             path: { "${params.outdir}/preprocessing/${meta.id}/markduplicates" },
             enabled: false
@@ -228,15 +228,17 @@ process {
         publishDir       = [
             path: { "${params.outdir}/preprocessing/${meta.id}/recal_table" },
             enabled: true,
-            pattern: "*recal.table"
+            mode: 'copy',
+            pattern: "*.table"
         ]
+        ext.prefix = {"${meta.id}.recal"}
     }
 }
 
 // RECALIBRATE
 process {
     withName: 'APPLYBQSR|APPLYBQSR_SPARK' {
-        ext.suffix       = '.recal'
+        ext.prefix = {"${meta.id}.recal"}
         publishDir       = [ enabled: false ]
     }
     withName: 'SAMTOOLS_MERGE_CRAM' {

modules.json

@@ -27,8 +27,32 @@
             "freebayes": {
                 "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
             },
+            "gatk4/applybqsr": {
+                "git_sha": "a6e0629e2430a9d4061ddc8afdf4cff8c93080b5"
+            },
+            "gatk4/baserecalibrator": {
+                "git_sha": "a6e0629e2430a9d4061ddc8afdf4cff8c93080b5"
+            },
             "gatk4/createsequencedictionary": {
-                "git_sha": "7389963d5cb18f81c10dff128c510e518ee4f0f6"
+                "git_sha": "50eafb19c689bca7747a6d44b8e7a555ba172f4b"
+            },
+            "gatk4/estimatelibrarycomplexity": {
+                "git_sha": "50eafb19c689bca7747a6d44b8e7a555ba172f4b"
+            },
+            "gatk4/gatherbqsrreports": {
+                "git_sha": "50eafb19c689bca7747a6d44b8e7a555ba172f4b"
+            },
+            "gatk4/genotypegvcfs": {
+                "git_sha": "a6e0629e2430a9d4061ddc8afdf4cff8c93080b5"
+            },
+            "gatk4/haplotypecaller": {
+                "git_sha": "a6e0629e2430a9d4061ddc8afdf4cff8c93080b5"
+            },
+            "gatk4/markduplicates": {
+                "git_sha": "50eafb19c689bca7747a6d44b8e7a555ba172f4b"
+            },
+            "gatk4/mutect2": {
+                "git_sha": "50eafb19c689bca7747a6d44b8e7a555ba172f4b"
             },
             "manta/germline": {
                 "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"