fixes

nf-cmgg · Oct 11, 2023 · 17b5ab0 · 17b5ab0
1 parent 27a6946
commit 17b5ab0
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Showing 38 changed files with 104 additions and 98 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -31,6 +31,8 @@ lint:
     - lib/NfcoreTemplate.groovy
     - .prettierignore
     - LICENSE
+  pipeline_name_conventions: false
+  actions_ci: false
 repository_type: pipeline
 template:
   author: nvnieuwk

diff --git a/conf/nf_test.config b/conf/nf_test.config
@@ -12,8 +12,8 @@ params {
     max_time        = '6.h'
 
     // Input data
-    input           = "${params.baseDir}/tests/inputs/samplesheet.csv"
-    outdir          = "${params.outputDir}"
+    input           = "${baseDir}/tests/inputs/samplesheet.csv"
+    outdir          = "${outputDir}"
 
     // Genome references
     genomes_ignore  = true

diff --git a/modules.json b/modules.json
@@ -39,12 +39,12 @@
                     },
                     "bcftools/sort": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "d6d112a1af2ee8c97fc1932df008183341e7d8fe",
                         "installed_by": ["vcf_annotate_ensemblvep_snpeff"]
                     },
                     "bcftools/stats": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "e2693a7e2d773b92e0649b25880ee22fe82bb79d",
                         "installed_by": ["modules"]
                     },
                     "bedtools/intersect": {
@@ -64,7 +64,7 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
                         "installed_by": ["modules"]
                     },
                     "ensemblvep/vep": {
@@ -75,33 +75,33 @@
                     },
                     "gatk4/calibratedragstrmodel": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/composestrtablefile": {
                         "branch": "master",
-                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",
-                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/genomicsdbimport": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/genotypegvcfs": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff"
                     },
                     "gatk4/haplotypecaller": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff"
                     },
@@ -117,12 +117,12 @@
                     },
                     "mosdepth": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "ebb27711cd5f4de921244bfa81c676504072d31c",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
                         "installed_by": ["modules"]
                     },
                     "rtgtools/format": {
@@ -169,7 +169,7 @@
                     },
                     "snpeff/snpeff": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "4d584d5cf6ed5f7363a51cdb4b3eb25398e9e537",
                         "installed_by": ["vcf_annotate_ensemblvep_snpeff"]
                     },
                     "somalier/extract": {
@@ -200,7 +200,7 @@
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
+                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
                         "installed_by": ["modules"]
                     },
                     "vardictjava": {

diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf
diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf
diff --git a/modules/nf-core/bcftools/stats/meta.yml b/modules/nf-core/bcftools/stats/meta.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff
diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf
diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf
diff --git a/modules/nf-core/gatk4/composestrtablefile/meta.yml b/modules/nf-core/gatk4/composestrtablefile/meta.yml
diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf
diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml
diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf
diff --git a/modules/nf-core/gatk4/genomicsdbimport/meta.yml b/modules/nf-core/gatk4/genomicsdbimport/meta.yml
diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf
diff --git a/modules/nf-core/gatk4/genotypegvcfs/meta.yml b/modules/nf-core/gatk4/genotypegvcfs/meta.yml
diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf
diff --git a/modules/nf-core/gatk4/haplotypecaller/meta.yml b/modules/nf-core/gatk4/haplotypecaller/meta.yml
diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf