From 9573e7e53de808736ab691ed7f4ed3d9758d62b1 Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Thu, 20 Jan 2022 19:00:20 +0100 Subject: [PATCH 1/3] Bump version 0.1.5 to chromap/chromap (#1223) * Bump version 0.1.5 to chromap/chromap * Bump conda samtools version to 1.14 * Get read of inconsistent md5sum in conda * Bump version in conda and retry md5 checks * genome index md5 hash removed, conda failed --- modules/chromap/chromap/main.nf | 16 ++++++++-------- tests/modules/chromap/chromap/test.yml | 9 +++------ tests/modules/chromap/index/test.yml | 2 ++ 3 files changed, 13 insertions(+), 14 deletions(-) diff --git a/modules/chromap/chromap/main.nf b/modules/chromap/chromap/main.nf index 4a7f0097..67384b0c 100644 --- a/modules/chromap/chromap/main.nf +++ b/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 """ } diff --git a/tests/modules/chromap/chromap/test.yml b/tests/modules/chromap/chromap/test.yml index 20a51e2b..09e5e753 100644 --- a/tests/modules/chromap/chromap/test.yml +++ b/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 diff --git a/tests/modules/chromap/index/test.yml b/tests/modules/chromap/index/test.yml index dde1aa1b..430a53b7 100644 --- a/tests/modules/chromap/index/test.yml +++ b/tests/modules/chromap/index/test.yml @@ -5,3 +5,5 @@ - chromap files: - path: output/chromap/genome.index + + From 55ea3f20618ba5630595164babc9a64c0a787080 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Fri, 21 Jan 2022 07:51:28 +0100 Subject: [PATCH 2/3] CI: print out pytest logs on failure (#1220) --- .github/workflows/pytest-workflow.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index cc7c9313..272e1f1d 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -93,6 +93,16 @@ 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 From 550df3b006ba7a68d7709311914e2cb1ca4aeb76 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 21 Jan 2022 06:57:57 +0000 Subject: [PATCH 3/3] ci: Remove second python setup call (#1225) Co-authored-by: Gregor Sturm --- .github/workflows/pytest-workflow.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 272e1f1d..ee922c45 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.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