Merge pull request nf-core#138 from maxulysse/gvcf

Adding gvcf

Author: maxulysse

.nf-core.yml

@@ -1 +1,13 @@
 repository_type: pipeline
+lint:
+  files_exist:
+    - lib/NfcoreTemplate.groovy
+    - lib/Utils.groovy
+    - lib/WorkflowMain.groovy
+    - lib/WorkflowRnavar.groovy
+  files_unchanged:
+    - .github/CONTRIBUTING.md
+    - .github/workflows/branch.yml
+    - .github/workflows/linting.yml
+    - .github/workflows/linting_comment.yml
+    - docs/images/nf-core-rnavar_logo_light.png

README.md

@@ -58,9 +58,6 @@
 > [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
-
 First, prepare a samplesheet with your input data that looks as follows:
 
 `samplesheet.csv`:
@@ -72,8 +69,6 @@ CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
 
--->
-
 Now, you can run the pipeline using:
 
 ```console
@@ -96,12 +91,23 @@ For more details about the output files and reports, please refer to the
 
 nf-core/rnavar was originally written in Nextflow DSL2 for use at the [Barntumörbanken, Karolinska Institutet](https://ki.se/forskning/barntumorbanken), by Praveen Raj ([@praveenraj2018](https://github.com/praveenraj2018)) and Maxime U Garcia ([@maxulysse](https://github.com/maxulysse)).
 
-The pipeline is primarily maintained by Praveen Raj ([@praveenraj2018](https://github.com/praveenraj2018)) from [Barntumörbanken, Karolinska Institutet](https://ki.se/forskning/barntumorbanken) and Maxime U Garcia ([@maxulysse](https://github.com/maxulysse)) from [Seqera Labs](https://seqera/io)
+nf-core/rnavar was originally written by Praveen Raj at [The Swedish Childhood Tumor Biobank (Barntumörbanken)](https://ki.se/forskning/barntumorbanken).
+Maxime U Garcia at [The Swedish Childhood Tumor Biobank (Barntumörbanken)](https://ki.se/forskning/barntumorbanken) helped with development.
+
+Maintenance is now lead by Maxime U Garcia (now at [Seqera Labs](https://seqera/io))
+
+Main developers:
+
+- [Maxime U Garcia](https://github.com/maxulysse)
+
+We thank the following people for their extensive assistance in the development of this pipeline:
 
-Many thanks to other who have helped out along the way too, including (but not limited to):
-[@ewels](https://github.com/ewels),
-[@drpatelh](https://github.com/drpatelh),
-[@nschcolnicov](https://github.com/nschcolnicov).
+- [Harshil Patel](https://github.com/drpatelh)
+- [Nicolás Schcolnicov](https://github.com/nschcolnicov)
+- [Ömer An](https://github.com/bounlu)
+- [Phil Ewels](https://github.com/ewels)
+- [Praveen Raj](https://github.com/praveenraj2018)
+- [Sarah Maman](https://github.com/SarahMaman)
 
 ## Contributions and Support
 

conf/modules.config

@@ -291,25 +291,12 @@ process {
     withName: GATK4_HAPLOTYPECALLER {
         ext.args    = [
             '--dont-use-soft-clipped-bases',
+            '--create-output-variant-index true',
             params.gatk_hc_call_conf ? "--standard-min-confidence-threshold-for-calling $params.gatk_hc_call_conf" : '',
-            params.bam_csi_index ? "--create-output-variant-index false" : ""
+            params.generate_gvcf ? "-ERC GVCF" : ""
         ].join(' ').trim()
         publishDir  = [ enabled: false ]
     }
-    withName: GATK4_HAPLOTYPECALLERGVCF {
-        ext.args    = [
-            '--dont-use-soft-clipped-bases',
-            params.gatk_hc_call_conf ? "--standard-min-confidence-threshold-for-calling $params.gatk_hc_call_conf" : '',
-            params.bam_csi_index ? "--create-output-variant-index false" : "", "-ERC GVCF"
-        ].join(' ').trim()
-        ext.prefix = {"${meta.id}.haplotypecaller"}
-        publishDir  = [ enabled: false ]
-    }
-    withName: GATK4_INDEXFEATUREFILE {
-        publishDir  = [
-            enabled: false
-        ]
-    }
 
     withName: GATK4_MERGEVCFS {
         ext.prefix  = {"${meta.id}.haplotypecaller"}