From 7026122ec8696016b0b81496d9d39a7918cdb5b2 Mon Sep 17 00:00:00 2001
From: Maxime Borry <maxibor@users.noreply.github.com>
Date: Mon, 31 Jan 2022 10:11:39 +0100
Subject: [PATCH] Freebayes: compress with bgzip (#1243)

* move to bgzip
* update freebayes test results
---
 modules/freebayes/main.nf        |  4 ++--
 tests/modules/freebayes/test.yml | 25 ++++++++++++++++++++-----
 2 files changed, 22 insertions(+), 7 deletions(-)

diff --git a/modules/freebayes/main.nf b/modules/freebayes/main.nf
index 1dd91fef..d462088a 100644
--- a/modules/freebayes/main.nf
+++ b/modules/freebayes/main.nf
@@ -41,7 +41,7 @@ process FREEBAYES {
             $args \\
             $input > ${prefix}.vcf
 
-        gzip --no-name ${prefix}.vcf
+        bgzip ${prefix}.vcf
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
@@ -60,7 +60,7 @@ process FREEBAYES {
             $args \\
             $input > ${prefix}.vcf
 
-        gzip --no-name ${prefix}.vcf
+        bgzip ${prefix}.vcf
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
diff --git a/tests/modules/freebayes/test.yml b/tests/modules/freebayes/test.yml
index c9aa78da..6cca692e 100644
--- a/tests/modules/freebayes/test.yml
+++ b/tests/modules/freebayes/test.yml
@@ -1,34 +1,49 @@
 - name: freebayes test_freebayes
-  command: nextflow run ./tests/modules/freebayes -entry test_freebayes -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
+  command: nextflow run tests/modules/freebayes -entry test_freebayes -c tests/config/nextflow.config
   tags:
     - freebayes
   files:
     - path: output/freebayes/test.vcf.gz
+      md5sum: 81d3e6ce7b6343d088b779567c3803eb
+    - path: output/freebayes/versions.yml
+      md5sum: 53651eb835af65df829241257584a7d2
 
 - name: freebayes test_freebayes_bed
-  command: nextflow run ./tests/modules/freebayes -entry test_freebayes_bed -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
+  command: nextflow run tests/modules/freebayes -entry test_freebayes_bed -c tests/config/nextflow.config
   tags:
     - freebayes
   files:
     - path: output/freebayes/test.vcf.gz
+      md5sum: 02645d014a63485162a7789007373b2a
+    - path: output/freebayes/versions.yml
+      md5sum: becc93c8a0be580c09d55b955d60a5e1
 
 - name: freebayes test_freebayes_cram
-  command: nextflow run ./tests/modules/freebayes -entry test_freebayes_cram -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
+  command: nextflow run tests/modules/freebayes -entry test_freebayes_cram -c tests/config/nextflow.config
   tags:
     - freebayes
   files:
     - path: output/freebayes/test.vcf.gz
+      md5sum: 3d0bfcd2129c62f8863952fa4c1054db
+    - path: output/freebayes/versions.yml
+      md5sum: 2e5b266edfc6cab81353cfc72c00f67c
 
 - name: freebayes test_freebayes_somatic
-  command: nextflow run ./tests/modules/freebayes -entry test_freebayes_somatic -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
+  command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic -c tests/config/nextflow.config
   tags:
     - freebayes
   files:
     - path: output/freebayes/test.vcf.gz
+      md5sum: 22fec868210ba3baf685b214bfd8e74b
+    - path: output/freebayes/versions.yml
+      md5sum: 8fbdb4c052fb3e42b5508a966125fa05
 
 - name: freebayes test_freebayes_somatic_cram_intervals
-  command: nextflow run ./tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
+  command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c tests/config/nextflow.config
   tags:
     - freebayes
   files:
     - path: output/freebayes/test.vcf.gz
+      md5sum: 527cf2937067bbd4117d95fd472bb928
+    - path: output/freebayes/versions.yml
+      md5sum: af97e3dfdc086188739907c3460e49e0