Merge branch 'nf-core:master' into maxquant

.github/workflows/pytest-workflow.yml

@@ -48,11 +48,6 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-pip-
 
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: "3.x"
-
       - name: Install Python dependencies
         run: python -m pip install --upgrade pip pytest-workflow
 
@@ -93,6 +88,16 @@ jobs:
         # only use one thread for pytest-workflow to avoid race condition on conda cache.
         run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
 
+      - name: Output log on failure
+        if: failure()
+        run: |
+          echo "======> log.out <======="
+          cat /home/runner/pytest_workflow_*/*/log.out
+          echo
+          echo
+          echo "======> log.err <======="
+          cat /home/runner/pytest_workflow_*/*/log.err
+
       - name: Upload logs on failure
         if: failure()
         uses: actions/upload-artifact@v2

modules/chromap/chromap/main.nf

@@ -1,13 +1,11 @@
-def VERSION = '0.1' // Version information not provided by tool on CLI
-
 process CHROMAP_CHROMAP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::chromap=0.1 bioconda::samtools=1.13" : null)
+    conda (params.enable_conda ? "bioconda::chromap=0.1.5 bioconda::samtools=1.14" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' :
-        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' :
+        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' }"
 
     input:
     tuple val(meta), path(reads)
@@ -45,7 +43,7 @@ process CHROMAP_CHROMAP {
         args_list << "--pairs-natural-chr-order $pairs_chr_order"
     }
     def final_args = args_list.join(' ')
-    def compression_cmds = "gzip ${prefix}.${file_extension}"
+    def compression_cmds = "gzip -n ${prefix}.${file_extension}"
     if (args.contains("--SAM")) {
         compression_cmds = """
         samtools view $args2 -@ $task.cpus -bh \\
@@ -67,7 +65,8 @@ process CHROMAP_CHROMAP {
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            chromap: $VERSION
+            chromap: \$(echo \$(chromap --version 2>&1))
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
         END_VERSIONS
         """
     } else {
@@ -85,7 +84,8 @@ process CHROMAP_CHROMAP {
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            chromap: $VERSION
+            chromap: \$(echo \$(chromap --version 2>&1))
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
         END_VERSIONS
         """
     }

tests/modules/chromap/chromap/test.yml

@@ -5,9 +5,8 @@
     - chromap
   files:
     - path: output/chromap/genome.index
-      md5sum: f889d5f61d80823766af33277d27d386
     - path: output/chromap/test.bed.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
+      md5sum: 25e40bde24c7b447292cd68573728694
 
 - name: chromap chromap test_chromap_chromap_paired_end
   command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@@ -16,9 +15,8 @@
     - chromap
   files:
     - path: output/chromap/genome.index
-      md5sum: f889d5f61d80823766af33277d27d386
     - path: output/chromap/test.bed.gz
-      md5sum: cafd8fb21977f5ae69e9008b220ab169
+      md5sum: 7cdc8448882b75811e0c784f5f20aef2
 
 - name: chromap chromap test_chromap_chromap_paired_bam
   command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@@ -27,6 +25,5 @@
     - chromap
   files:
     - path: output/chromap/genome.index
-      md5sum: f889d5f61d80823766af33277d27d386
     - path: output/chromap/test.bam
-      md5sum: bd1e3fe0f3abd1430ae191754f16a3ed
+      md5sum: 73e2c76007e3c61df625668e01b3f42f

tests/modules/chromap/index/test.yml

@@ -5,3 +5,5 @@
     - chromap
   files:
     - path: output/chromap/genome.index
+
+