From 20a0055dcd9ad8b4f6aed3f0acf9ae41e460d833 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Tue, 10 Dec 2024 01:03:08 +0000 Subject: [PATCH 1/3] update confirm-pass jobs to correctly identify failed & cancelled --- .github/workflows/gpu-tests.yml | 11 ++++++++--- .github/workflows/nf-test.yml | 11 ++++++++--- 2 files changed, 16 insertions(+), 6 deletions(-) diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml index 78667065a3b..88c04a3ef81 100644 --- a/.github/workflows/gpu-tests.yml +++ b/.github/workflows/gpu-tests.yml @@ -108,13 +108,18 @@ jobs: needs: [nf-test-gpu] if: always() steps: - - name: All tests ok - if: ${{ success() || !contains(needs.*.result, 'failure') }} - run: exit 0 - name: One or more tests failed if: ${{ contains(needs.*.result, 'failure') }} run: exit 1 + - name: One or more tests cancelled + if: ${{ contains(needs.*.result, 'cancelled') }} + run: exit 1 + + - name: All tests ok + if: ${{ contains(needs.*.result, 'success') }} + run: exit 0 + - name: debug-print if: always() run: | diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index f8c71275bf9..9d3aa1e5b6d 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -110,13 +110,18 @@ jobs: needs: [nf-test] if: always() steps: - - name: All tests ok - if: ${{ success() || !contains(needs.*.result, 'failure') }} - run: exit 0 - name: One or more tests failed if: ${{ contains(needs.*.result, 'failure') }} run: exit 1 + - name: One or more tests cancelled + if: ${{ contains(needs.*.result, 'cancelled') }} + run: exit 1 + + - name: All tests ok + if: ${{ contains(needs.*.result, 'success') }} + run: exit 0 + - name: debug-print if: always() run: | From 2d75d8e8391e1d98e398ce5bd2bbf66b4ccc51f6 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Tue, 10 Dec 2024 01:03:38 +0000 Subject: [PATCH 2/3] touch gpu & cpu module to test --- .../nf-core/bwameth/align/tests/main.nf.test | 1 - modules/nf-core/parabricks/fq2bammeth/main.nf | 14 ++++---- .../parabricks/fq2bammeth/tests/main.nf.test | 9 +++--- .../fq2bammeth/tests/main.nf.test.snap | 32 +++++++++---------- 4 files changed, 28 insertions(+), 28 deletions(-) diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test b/modules/nf-core/bwameth/align/tests/main.nf.test index 37dd4ad2b08..87195e0c31a 100644 --- a/modules/nf-core/bwameth/align/tests/main.nf.test +++ b/modules/nf-core/bwameth/align/tests/main.nf.test @@ -117,5 +117,4 @@ nextflow_process { ) } } - } diff --git a/modules/nf-core/parabricks/fq2bammeth/main.nf b/modules/nf-core/parabricks/fq2bammeth/main.nf index 44f266604bd..eb7ae685b71 100644 --- a/modules/nf-core/parabricks/fq2bammeth/main.nf +++ b/modules/nf-core/parabricks/fq2bammeth/main.nf @@ -27,14 +27,15 @@ process PARABRICKS_FQ2BAMMETH { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead." } - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def in_fq_command = meta.single_end ? "--in-se-fq $reads" : "--in-fq $reads" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def in_fq_command = meta.single_end ? "--in-se-fq $reads" : "--in-fq $reads" def known_sites_command = known_sites ? known_sites.collect{"--knownSites $it"}.join(' ') : "" - def known_sites_output = known_sites ? "--out-recal-file ${prefix}.table" : "" - def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : '' + def known_sites_output = known_sites ? "--out-recal-file ${prefix}.table" : "" + def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : '' """ ln -sf \$(readlink $fasta) $index/$fasta + pbrun \\ fq2bam_meth \\ --ref $index/$fasta \\ @@ -44,6 +45,7 @@ process PARABRICKS_FQ2BAMMETH { $known_sites_output \\ $num_gpus \\ $args + cat <<-END_VERSIONS > versions.yml "${task.process}": pbrun: \$(echo \$(pbrun version 2>&1) | sed 's/^Please.* //' ) @@ -55,11 +57,11 @@ process PARABRICKS_FQ2BAMMETH { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead." } - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bam touch ${prefix}.bam.bai + cat <<-END_VERSIONS > versions.yml "${task.process}": pbrun: \$(echo \$(pbrun version 2>&1) | sed 's/^Please.* //' ) diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test index 459eb6317db..ce89e8cac9f 100644 --- a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test +++ b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test @@ -5,12 +5,12 @@ nextflow_process { process "PARABRICKS_FQ2BAMMETH" config "./nextflow.config" + tag "gpu" tag "bwameth/index" tag "modules" tag "parabricks" tag "parabricks/fq2bammeth" tag "modules_nfcore" - tag "gpu" setup { run("BWAMETH_INDEX") { @@ -26,8 +26,7 @@ nextflow_process { } } - - test("SRR389222 - fastq - se") { + test("SRR389222 single-end [fastq]") { when { process { @@ -60,7 +59,7 @@ nextflow_process { } } - test("SRR389222 - fastq - se - stub") { + test("SRR389222 single-end [fastq] - stub") { options '-stub' when { @@ -90,7 +89,7 @@ nextflow_process { } } - test("E. coli - fastq - pe - stub") { + test("E.coli paired-end [fastq] - stub") { options '-stub' when { diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap index cf06f28c7b3..21ae222c254 100644 --- a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "SRR389222 - fastq - se - stub": { + "SRR389222 single-end [fastq] - stub": { "content": [ { "0": [ @@ -21,13 +21,13 @@ ] ], "2": [ - + ], "3": [ - + ], "4": [ - + ], "5": [ "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf" @@ -51,13 +51,13 @@ ] ], "bqsr_table": [ - + ], "duplicate_metrics": [ - + ], "qc_metrics": [ - + ], "versions": [ "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf" @@ -70,7 +70,7 @@ }, "timestamp": "2024-11-12T11:20:10.809580487" }, - "E. coli - fastq - pe - stub": { + "E.coli paired-end [fastq] - stub": { "content": [ { "0": [ @@ -92,13 +92,13 @@ ] ], "2": [ - + ], "3": [ - + ], "4": [ - + ], "5": [ "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf" @@ -122,13 +122,13 @@ ] ], "bqsr_table": [ - + ], "duplicate_metrics": [ - + ], "qc_metrics": [ - + ], "versions": [ "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf" @@ -141,7 +141,7 @@ }, "timestamp": "2024-11-12T11:20:18.927598721" }, - "SRR389222 - fastq - se": { + "SRR389222 single-end [fastq]": { "content": [ "a7f7ca7b5eb503ab58790d64a0273ed6", [ @@ -163,4 +163,4 @@ }, "timestamp": "2024-10-26T21:29:14.709022" } -} \ No newline at end of file +} From f9a38d331b6acadc94e69ea1af9a38434ec2630c Mon Sep 17 00:00:00 2001 From: Sateesh Date: Tue, 10 Dec 2024 11:12:20 +0000 Subject: [PATCH 3/3] bump NXF VER to 24.10.2 --- .github/workflows/gpu-tests.yml | 2 +- .github/workflows/nf-test.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml index 88c04a3ef81..2a341360f04 100644 --- a/.github/workflows/gpu-tests.yml +++ b/.github/workflows/gpu-tests.yml @@ -29,7 +29,7 @@ env: NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver - NXF_VER: "24.10.1" + NXF_VER: "24.10.2" jobs: nf-test-changes: diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 9d3aa1e5b6d..036c40f0880 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -32,7 +32,7 @@ env: NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver - NXF_VER: "24.10.1" + NXF_VER: "24.10.2" jobs: nf-test-changes: