Update version strings (nf-core#4556)

* Update version extraction string * Update umitools version string extraction * Fix umitools/dedup pytest * Fix umitools/group pytest * Update umitools/extract snapshot * Fix formatting
maxulysse · Dec 8, 2023 · 65ad3e0 · 65ad3e0
1 parent 1bfd681
commit 65ad3e0
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Showing 7 changed files with 75 additions and 46 deletions.
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
@@ -37,7 +37,7 @@ process FASTQC {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
     END_VERSIONS
     """
 
@@ -49,7 +49,7 @@ process FASTQC {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf
@@ -42,7 +42,7 @@ process UMITOOLS_DEDUP {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
+        umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
     END_VERSIONS
     """
 
@@ -56,7 +56,7 @@ process UMITOOLS_DEDUP {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
+        umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf
@@ -33,7 +33,7 @@ process UMITOOLS_EXTRACT {
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
+            umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
         END_VERSIONS
         """
     }  else {
@@ -49,7 +49,7 @@ process UMITOOLS_EXTRACT {
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
+            umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
         END_VERSIONS
         """
     }

diff --git a/modules/nf-core/umitools/extract/tests/main.nf.test.snap b/modules/nf-core/umitools/extract/tests/main.nf.test.snap
diff --git a/modules/nf-core/umitools/group/main.nf b/modules/nf-core/umitools/group/main.nf
@@ -43,7 +43,7 @@ process UMITOOLS_GROUP {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
+        umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
     END_VERSIONS
     """
 
@@ -56,7 +56,7 @@ process UMITOOLS_GROUP {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
+        umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
     END_VERSIONS
     """
 }
diff --git a/tests/modules/nf-core/umitools/dedup/test.yml b/tests/modules/nf-core/umitools/dedup/test.yml
@@ -1,18 +1,22 @@
 - name: umitools dedup test_umitools_dedup_no_umi
-  command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_no_umi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/umitools/dedup/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_no_umi -c ./tests/config/nextflow.config
   tags:
-    - umitools/dedup
     - umitools
+    - umitools/dedup
   files:
     - path: output/umitools/test.dedup.bam
       md5sum: 350e942a0d45e8356fa24bc8c47dc1ed
+    - path: output/umitools/test.dedup.log
+      contains:
+        - "# UMI-tools version:"
+        - "job finished"
     - path: output/umitools/versions.yml
 
 - name: umitools dedup test_umitools_dedup_single_end_no_stats
-  command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_single_end_no_stats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/umitools/dedup/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_single_end_no_stats -c ./tests/config/nextflow.config
   tags:
-    - umitools/dedup
     - umitools
+    - umitools/dedup
   files:
     - path: output/bwa/bwa/genome.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
@@ -25,24 +29,29 @@
     - path: output/bwa/bwa/genome.sa
       md5sum: ab3952cabf026b48cd3eb5bccbb636d1
     - path: output/bwa/test.bam
-      md5sum: af925e0019ce03eb8716ad3f8471311d
+      md5sum: 68041e4508f9e0c32ed48195f611fe97
     - path: output/bwa/versions.yml
     - path: output/samtools/test.bam.bai
-      md5sum: 4db1993dbd1ad8bbe3c5eea6d7ee6136
+      md5sum: dc4badbb66bd19a56ed135755387877e
     - path: output/samtools/versions.yml
     - path: output/umitools/test.dedup.bam
-      md5sum: 9541c6ac00eea9064786244be9d8738f
+      md5sum: 25c6809dfff16f14da5eeeecb5c2018f
+    - path: output/umitools/test.dedup.log
+      contains:
+        - "# UMI-tools version:"
+        - "job finished"
+    - path: output/umitools/test.umi_extract.fastq.gz
     - path: output/umitools/test.umi_extract.log
-      contains: ["Starting barcode extraction"]
+      contains:
+        - "# UMI-tools version:"
+        - "job finished"
     - path: output/umitools/versions.yml
-    - path: output/umitools/test.dedup.log
-      contains: ["# UMI-tools version:"]
 
 - name: umitools dedup test_umitools_dedup_paired_end_no_stats
-  command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_paired_end_no_stats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/umitools/dedup/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_paired_end_no_stats -c ./tests/config/nextflow.config
   tags:
-    - umitools/dedup
     - umitools
+    - umitools/dedup
   files:
     - path: output/bwa/bwa/genome.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
@@ -55,24 +64,30 @@
     - path: output/bwa/bwa/genome.sa
       md5sum: ab3952cabf026b48cd3eb5bccbb636d1
     - path: output/bwa/test.bam
-      md5sum: 82063366bc9e8935f3c10d863b03f719
+      md5sum: 2211b0bf184d44519d0a6f9ad20456ba
     - path: output/bwa/versions.yml
     - path: output/samtools/test.bam.bai
-      md5sum: b63b387c59f0fa8fbc24c9faf613240a
+      md5sum: 6cae374413a2823191543ee7eba81a58
     - path: output/samtools/versions.yml
     - path: output/umitools/test.dedup.bam
-      md5sum: 1bf0f4849aa8b488f1f1a86135e25a16
+      md5sum: 53304928c301ca69c6d079600ff07ce0
+    - path: output/umitools/test.dedup.log
+      contains:
+        - "# UMI-tools version:"
+        - "job finished"
     - path: output/umitools/test.umi_extract.log
-      contains: ["Starting barcode extraction"]
+      contains:
+        - "# UMI-tools version:"
+        - "job finished"
+    - path: output/umitools/test.umi_extract_1.fastq.gz
+    - path: output/umitools/test.umi_extract_2.fastq.gz
     - path: output/umitools/versions.yml
-    - path: output/umitools/test.dedup.log
-      contains: ["# UMI-tools version:"]
 
 - name: umitools dedup test_umitools_dedup_paired_end_stats
-  command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_paired_end_stats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/umitools/dedup/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_paired_end_stats -c ./tests/config/nextflow.config
   tags:
-    - umitools/dedup
     - umitools
+    - umitools/dedup
   files:
     - path: output/bwa/bwa/genome.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
@@ -85,21 +100,27 @@
     - path: output/bwa/bwa/genome.sa
       md5sum: ab3952cabf026b48cd3eb5bccbb636d1
     - path: output/bwa/test.bam
-      md5sum: 82063366bc9e8935f3c10d863b03f719
+      md5sum: 2211b0bf184d44519d0a6f9ad20456ba
     - path: output/bwa/versions.yml
     - path: output/samtools/test.bam.bai
-      md5sum: b63b387c59f0fa8fbc24c9faf613240a
+      md5sum: 6cae374413a2823191543ee7eba81a58
     - path: output/samtools/versions.yml
     - path: output/umitools/test.dedup.bam
-      md5sum: 1bf0f4849aa8b488f1f1a86135e25a16
+      md5sum: 53304928c301ca69c6d079600ff07ce0
+    - path: output/umitools/test.dedup.log
+      contains:
+        - "# UMI-tools version:"
+        - "job finished"
     - path: output/umitools/test.dedup_edit_distance.tsv
       md5sum: c247a49b58768e6e2e86a6c08483e612
     - path: output/umitools/test.dedup_per_umi.tsv
       md5sum: 10e35ca37f2bfb521ac6dd7314951a68
     - path: output/umitools/test.dedup_per_umi_per_position.tsv
       md5sum: 2e1a12e6f720510880068deddeefe063
     - path: output/umitools/test.umi_extract.log
-      contains: ["Starting barcode extraction"]
+      contains:
+        - "# UMI-tools version:"
+        - "job finished"
+    - path: output/umitools/test.umi_extract_1.fastq.gz
+    - path: output/umitools/test.umi_extract_2.fastq.gz
     - path: output/umitools/versions.yml
-    - path: output/umitools/test.dedup.log
-      contains: ["# UMI-tools version:"]
diff --git a/tests/modules/nf-core/umitools/group/test.yml b/tests/modules/nf-core/umitools/group/test.yml
@@ -1,51 +1,59 @@
 - name: umitools group test_umitools_group_no_umi
-  command: nextflow run ./tests/modules/nf-core/umitools/group -entry test_umitools_group_no_umi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/umitools/group/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/umitools/group -entry test_umitools_group_no_umi -c ./tests/config/nextflow.config
   tags:
     - umitools/group
     - umitools
   files:
     - path: output/umitools/test.group.bam
       md5sum: fb90b49a90c2b3e8ddfedd9c95361625
     - path: output/umitools/test.group.log
-      contains: ["# UMI-tools version:"]
+      contains:
+        - "# UMI-tools version:"
+        - "job finished"
     - path: output/umitools/test.group.tsv
       md5sum: 1a3ccdc00df59fa89c79ad482980a003
     - path: output/umitools/versions.yml
 
 - name: umitools group test_umitools_group_single_end_info
-  command: nextflow run ./tests/modules/nf-core/umitools/group -entry test_umitools_group_single_end_info -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/umitools/group/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/umitools/group -entry test_umitools_group_single_end_info -c ./tests/config/nextflow.config
   tags:
     - umitools/group
     - umitools
   files:
     - path: output/umitools/test.group.log
-      contains: ["# UMI-tools version:"]
+      contains:
+        - "# UMI-tools version:"
+        - "job finished"
     - path: output/umitools/test.group.tsv
       md5sum: e7d46166eb3d8f42d73032e44f313b71
     - path: output/umitools/versions.yml
 
 - name: umitools group test_umitools_group_paired_end_bam
-  command: nextflow run ./tests/modules/nf-core/umitools/group -entry test_umitools_group_paired_end_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/umitools/group/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/umitools/group -entry test_umitools_group_paired_end_bam -c ./tests/config/nextflow.config
   tags:
     - umitools/group
     - umitools
   files:
     - path: output/umitools/test.group.bam
-      md5sum: 8f9250416a7ccbe970f5034826c318f5
+      md5sum: 939c7ab9c5c7f78c2664b152b76fead4
     - path: output/umitools/test.group.log
-      contains: ["# UMI-tools version:"]
+      contains:
+        - "# UMI-tools version:"
+        - "job finished"
     - path: output/umitools/versions.yml
 
 - name: umitools group test_umitools_group_paired_bam_info
-  command: nextflow run ./tests/modules/nf-core/umitools/group -entry test_umitools_group_paired_bam_info -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/umitools/group/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/umitools/group -entry test_umitools_group_paired_bam_info -c ./tests/config/nextflow.config
   tags:
     - umitools/group
     - umitools
   files:
     - path: output/umitools/test.group.bam
-      md5sum: 8f9250416a7ccbe970f5034826c318f5
+      md5sum: 939c7ab9c5c7f78c2664b152b76fead4
     - path: output/umitools/test.group.log
-      contains: ["# UMI-tools version:"]
+      contains:
+        - "# UMI-tools version:"
+        - "job finished"
     - path: output/umitools/test.group.tsv
       md5sum: d652eb6570057e9e709e8cac5f43d00c
     - path: output/umitools/versions.yml