From ecece498f10b47b7c9d06f53a310cea5811b4c5f Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 16 Jun 2022 13:42:01 +0200
Subject: [PATCH] samtools/*stats*: use prefix for outputs (#1788)

* use prefix in flagstat

* use prefix in idxstats

* use prefix in stats

* update test.yml
---
 modules/samtools/flagstat/main.nf        |  3 ++-
 modules/samtools/idxstats/main.nf        |  4 +++-
 modules/samtools/stats/main.nf           |  9 +++++----
 tests/modules/samtools/flagstat/test.yml |  6 +++---
 tests/modules/samtools/idxstats/test.yml |  8 ++++----
 tests/modules/samtools/stats/test.yml    | 12 ++++++------
 6 files changed, 23 insertions(+), 19 deletions(-)

diff --git a/modules/samtools/flagstat/main.nf b/modules/samtools/flagstat/main.nf
index b87b2108..03ec2dcf 100644
--- a/modules/samtools/flagstat/main.nf
+++ b/modules/samtools/flagstat/main.nf
@@ -19,12 +19,13 @@ process SAMTOOLS_FLAGSTAT {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     samtools \\
         flagstat \\
         --threads ${task.cpus-1} \\
         $bam \\
-        > ${bam}.flagstat
+        > ${prefix}.flagstat
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/samtools/idxstats/main.nf b/modules/samtools/idxstats/main.nf
index a49ff35f..4b245419 100644
--- a/modules/samtools/idxstats/main.nf
+++ b/modules/samtools/idxstats/main.nf
@@ -19,11 +19,13 @@ process SAMTOOLS_IDXSTATS {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
     """
     samtools \\
         idxstats \\
         $bam \\
-        > ${bam}.idxstats
+        > ${prefix}.idxstats
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/samtools/stats/main.nf b/modules/samtools/stats/main.nf
index bbdc3240..c913bc5e 100644
--- a/modules/samtools/stats/main.nf
+++ b/modules/samtools/stats/main.nf
@@ -8,7 +8,7 @@ process SAMTOOLS_STATS {
         'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
-    tuple val(meta), path(input), path(input_index)
+    tuple val(meta), path(bam), path(bai)
     path fasta
 
     output:
@@ -20,14 +20,15 @@ process SAMTOOLS_STATS {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     def reference = fasta ? "--reference ${fasta}" : ""
     """
     samtools \\
         stats \\
         --threads ${task.cpus-1} \\
         ${reference} \\
-        ${input} \\
-        > ${input}.stats
+        ${bam} \\
+        > ${prefix}.stats
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -38,7 +39,7 @@ process SAMTOOLS_STATS {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${input}.stats
+    touch ${prefix}.stats
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/samtools/flagstat/test.yml b/tests/modules/samtools/flagstat/test.yml
index a5f28b36..31762434 100644
--- a/tests/modules/samtools/flagstat/test.yml
+++ b/tests/modules/samtools/flagstat/test.yml
@@ -1,8 +1,8 @@
-- name: samtools flagstat
-  command: nextflow run ./tests/modules/samtools/flagstat -entry test_samtools_flagstat -c ./tests/config/nextflow.config -c ./tests/modules/samtools/flagstat/nextflow.config
+- name: samtools flagstat test_samtools_flagstat
+  command: nextflow run ./tests/modules/samtools/flagstat -entry test_samtools_flagstat -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/flagstat/nextflow.config
   tags:
     - samtools
     - samtools/flagstat
   files:
-    - path: ./output/samtools/test.paired_end.sorted.bam.flagstat
+    - path: output/samtools/test.flagstat
       md5sum: 4f7ffd1e6a5e85524d443209ac97d783
diff --git a/tests/modules/samtools/idxstats/test.yml b/tests/modules/samtools/idxstats/test.yml
index 88786eef..84a65dbd 100644
--- a/tests/modules/samtools/idxstats/test.yml
+++ b/tests/modules/samtools/idxstats/test.yml
@@ -1,8 +1,8 @@
-- name: samtools idxstats
-  command: nextflow run ./tests/modules/samtools/idxstats -entry test_samtools_idxstats -c ./tests/config/nextflow.config -c ./tests/modules/samtools/idxstats/nextflow.config
+- name: samtools idxstats test_samtools_idxstats
+  command: nextflow run ./tests/modules/samtools/idxstats -entry test_samtools_idxstats -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/idxstats/nextflow.config
   tags:
-    - samtools
     - samtools/idxstats
+    - samtools
   files:
-    - path: ./output/samtools/test.paired_end.sorted.bam.idxstats
+    - path: output/samtools/test.idxstats
       md5sum: df60a8c8d6621100d05178c93fb053a2
diff --git a/tests/modules/samtools/stats/test.yml b/tests/modules/samtools/stats/test.yml
index 304619ee..be6c3ccc 100644
--- a/tests/modules/samtools/stats/test.yml
+++ b/tests/modules/samtools/stats/test.yml
@@ -1,17 +1,17 @@
 - name: samtools stats test_samtools_stats
-  command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config
+  command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/stats/nextflow.config
   tags:
-    - samtools/stats
     - samtools
+    - samtools/stats
   files:
-    - path: output/samtools/test.paired_end.sorted.bam.stats
+    - path: output/samtools/test.stats
       md5sum: c1e9ad551281b0bca32be1c832d125af
 
 - name: samtools stats test_samtools_stats_cram
-  command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config
+  command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/stats/nextflow.config
   tags:
-    - samtools/stats
     - samtools
+    - samtools/stats
   files:
-    - path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats
+    - path: output/samtools/test.stats
       md5sum: 103cd7b19743c42dab9ce570144c6f36