From 3a42289c3a55752ba7d7d9907b333f6e50b3402b Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Wed, 17 Sep 2025 11:11:46 -0400 Subject: [PATCH 01/15] tests: commit empty FASTQs --- tests/input/README.md | 8 ++++++++ tests/input/empty.r1.fq.gz | 3 +++ tests/input/empty.r2.fq.gz | 3 +++ 3 files changed, 14 insertions(+) create mode 100644 tests/input/empty.r1.fq.gz create mode 100644 tests/input/empty.r2.fq.gz diff --git a/tests/input/README.md b/tests/input/README.md index d03cdd5da..feef40063 100644 --- a/tests/input/README.md +++ b/tests/input/README.md @@ -40,6 +40,14 @@ Intervals for `chr1` (and one interval from `chr19`) derived from `wgs_calling_r Combined beta values from `minfi` for two patient samples. +## empty.r1.fq.gz + +A gzipped FASTQ file without any reads inside. + +## empty.r2.fq.gz + +A gzipped FASTQ file without any reads inside. + ## filtered_beta.csv Beta values from `minfi` filtered to the top 10K most differentially methylated probes. diff --git a/tests/input/empty.r1.fq.gz b/tests/input/empty.r1.fq.gz new file mode 100644 index 000000000..9badddd05 --- /dev/null +++ b/tests/input/empty.r1.fq.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ac73670af3abed54ac6fb4695131f4099be9fbe39d6076c5d0264a6bbdae9d83 +size 20 diff --git a/tests/input/empty.r2.fq.gz b/tests/input/empty.r2.fq.gz new file mode 100644 index 000000000..9badddd05 --- /dev/null +++ b/tests/input/empty.r2.fq.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ac73670af3abed54ac6fb4695131f4099be9fbe39d6076c5d0264a6bbdae9d83 +size 20 From e07fc13457ec076ad6324d40804e6c6f5bf1a14b Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Wed, 17 Sep 2025 11:26:52 -0400 Subject: [PATCH 02/15] tests: commit empty BAM --- tests/input/README.md | 4 ++++ tests/input/empty.Aligned.out.bam | 3 +++ 2 files changed, 7 insertions(+) create mode 100644 tests/input/empty.Aligned.out.bam diff --git a/tests/input/README.md b/tests/input/README.md index feef40063..8e395d896 100644 --- a/tests/input/README.md +++ b/tests/input/README.md @@ -40,6 +40,10 @@ Intervals for `chr1` (and one interval from `chr19`) derived from `wgs_calling_r Combined beta values from `minfi` for two patient samples. +## empty.Aligned.out.bam + +The result of passing `empty.r[1,2].fq.gz` into STAR alignment. + ## empty.r1.fq.gz A gzipped FASTQ file without any reads inside. diff --git a/tests/input/empty.Aligned.out.bam b/tests/input/empty.Aligned.out.bam new file mode 100644 index 000000000..9d96f9b73 --- /dev/null +++ b/tests/input/empty.Aligned.out.bam @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e9b67b09b4957e3b0496611bf2cdba1f58a91d27e7c07c015081f624ef831079 +size 2062 From e75a3d5f92793ddefd832d25c3cbb9078782206b Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Wed, 17 Sep 2025 11:27:25 -0400 Subject: [PATCH 03/15] Update .gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 4e1ba9e0c..eac267b03 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,6 @@ # Ignore common bioinformatics formats used in these workflows. **/*.fastq.gz +**/*.fq.gz **/*.fa **/*.gtf **/*.bam From 7b1c1041ef206865076cc5b382dcbefc04f376cc Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Wed, 17 Sep 2025 11:34:22 -0400 Subject: [PATCH 04/15] tests: commit gzipped Y+M fa --- tests/input/GRCh38.chrY_chrM.fa.gz | 3 +++ tests/input/README.md | 4 ++++ 2 files changed, 7 insertions(+) create mode 100644 tests/input/GRCh38.chrY_chrM.fa.gz diff --git a/tests/input/GRCh38.chrY_chrM.fa.gz b/tests/input/GRCh38.chrY_chrM.fa.gz new file mode 100644 index 000000000..7c87e51af --- /dev/null +++ b/tests/input/GRCh38.chrY_chrM.fa.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c24bb220de848ea993a67841ca9de65c3c6bb2783a2abbb03cfb75a09a429af4 +size 7060411 diff --git a/tests/input/README.md b/tests/input/README.md index 8e395d896..53478acce 100644 --- a/tests/input/README.md +++ b/tests/input/README.md @@ -108,6 +108,10 @@ FASTA format GRCh38 reference containing `chrY` and `chrM` only FASTA index for GRCh38 reference containing `chrY` and `chrM` only +## GRCh38.chrY_chrM.fa.gz + +Gzipped `GRCh38.chrY_chrM.fa` + ## Homo_sapiens_assembly38.dbsnp138.top5000.vcf First 5000 records for hg38 from dbsnp version 138. From d1587f54761434f9df013c25260244939b8d360e Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Wed, 17 Sep 2025 13:17:10 -0400 Subject: [PATCH 05/15] WIP --- ...empty.Aligned.out.bam => empty.chrY_chrM.Aligned.out.bam | 0 tests/input/README.md | 6 +++++- tests/input/empty.chrY_chrM.bwa_aln.bam | 3 +++ 3 files changed, 8 insertions(+), 1 deletion(-) rename tests/input/empty.Aligned.out.bam => empty.chrY_chrM.Aligned.out.bam (100%) create mode 100644 tests/input/empty.chrY_chrM.bwa_aln.bam diff --git a/tests/input/empty.Aligned.out.bam b/empty.chrY_chrM.Aligned.out.bam similarity index 100% rename from tests/input/empty.Aligned.out.bam rename to empty.chrY_chrM.Aligned.out.bam diff --git a/tests/input/README.md b/tests/input/README.md index 53478acce..767507123 100644 --- a/tests/input/README.md +++ b/tests/input/README.md @@ -40,10 +40,14 @@ Intervals for `chr1` (and one interval from `chr19`) derived from `wgs_calling_r Combined beta values from `minfi` for two patient samples. -## empty.Aligned.out.bam +## empty.chrY_chrM.Aligned.out.bam The result of passing `empty.r[1,2].fq.gz` into STAR alignment. +## empty.chrY_chrM.bwa_aln.bam + +The result of passing `empty.r[1,2].fq.gz` into BWA aln alignment. + ## empty.r1.fq.gz A gzipped FASTQ file without any reads inside. diff --git a/tests/input/empty.chrY_chrM.bwa_aln.bam b/tests/input/empty.chrY_chrM.bwa_aln.bam new file mode 100644 index 000000000..dfc0acc66 --- /dev/null +++ b/tests/input/empty.chrY_chrM.bwa_aln.bam @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b98c4e371b1a725a5a7d785ee52c063454e540307ee1f53daca880d9378c08b0 +size 281 From 85122e99027b70a86c3f063c9e799133b18b44c8 Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Wed, 17 Sep 2025 13:18:27 -0400 Subject: [PATCH 06/15] Update pytest.yaml --- .github/workflows/pytest.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml index 74a96b40b..77e66b6e5 100644 --- a/.github/workflows/pytest.yaml +++ b/.github/workflows/pytest.yaml @@ -33,7 +33,7 @@ jobs: - name: Build Sprocket if: matrix.runner == 'sprocket' run: | - cargo install sprocket --locked + cargo install --git https://github.com/peterhuene/sprocket --branch fix-perms - name: Set up Python uses: actions/setup-python@v5 with: From 138fa4cf6e9431ab6bc4f49e23c19d747ea60a52 Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Wed, 17 Sep 2025 14:08:51 -0400 Subject: [PATCH 07/15] Revert "Update pytest.yaml" This reverts commit 85122e99027b70a86c3f063c9e799133b18b44c8. --- .github/workflows/pytest.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml index 77e66b6e5..74a96b40b 100644 --- a/.github/workflows/pytest.yaml +++ b/.github/workflows/pytest.yaml @@ -33,7 +33,7 @@ jobs: - name: Build Sprocket if: matrix.runner == 'sprocket' run: | - cargo install --git https://github.com/peterhuene/sprocket --branch fix-perms + cargo install sprocket --locked - name: Set up Python uses: actions/setup-python@v5 with: From a7d933efbe06a378a71d0b1f926234f2152fcb1b Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Wed, 17 Sep 2025 16:20:10 -0400 Subject: [PATCH 08/15] Delete empty.chrY_chrM.Aligned.out.bam --- empty.chrY_chrM.Aligned.out.bam | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 empty.chrY_chrM.Aligned.out.bam diff --git a/empty.chrY_chrM.Aligned.out.bam b/empty.chrY_chrM.Aligned.out.bam deleted file mode 100644 index 9d96f9b73..000000000 --- a/empty.chrY_chrM.Aligned.out.bam +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:e9b67b09b4957e3b0496611bf2cdba1f58a91d27e7c07c015081f624ef831079 -size 2062 From e2001d5f532701bc50a340fada81eaeb909417ad Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Wed, 17 Sep 2025 16:20:43 -0400 Subject: [PATCH 09/15] Create empty.chrY_chrM.Aligned.out.bam --- tests/input/empty.chrY_chrM.Aligned.out.bam | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 tests/input/empty.chrY_chrM.Aligned.out.bam diff --git a/tests/input/empty.chrY_chrM.Aligned.out.bam b/tests/input/empty.chrY_chrM.Aligned.out.bam new file mode 100644 index 000000000..9d96f9b73 --- /dev/null +++ b/tests/input/empty.chrY_chrM.Aligned.out.bam @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e9b67b09b4957e3b0496611bf2cdba1f58a91d27e7c07c015081f624ef831079 +size 2062 From a90340a54c217b8d02d2309642746eb39db43991 Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Wed, 17 Sep 2025 16:21:59 -0400 Subject: [PATCH 10/15] Update .gitignore --- .gitignore | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/.gitignore b/.gitignore index eac267b03..dccc1afd1 100644 --- a/.gitignore +++ b/.gitignore @@ -1,11 +1,12 @@ # Ignore common bioinformatics formats used in these workflows. -**/*.fastq.gz -**/*.fq.gz -**/*.fa -**/*.gtf -**/*.bam -**/*.sam -**/*.log +# But only if they are in the root of this repo +/*.fastq.gz +/*.fq.gz +/*.fa +/*.gtf +/*.bam +/*.sam +/*.log # Ignore Cromwell, Womtool, Sprocket, and miniwdl files **/cromwell* From 51b819f7d3fdb42bfe8d2274460a6f8d04a4beef Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Wed, 17 Sep 2025 16:25:41 -0400 Subject: [PATCH 11/15] Update empty.chrY_chrM.bwa_aln.SE.bam --- ...empty.chrY_chrM.bwa_aln.bam => empty.chrY_chrM.bwa_aln.SE.bam} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename tests/input/{empty.chrY_chrM.bwa_aln.bam => empty.chrY_chrM.bwa_aln.SE.bam} (100%) diff --git a/tests/input/empty.chrY_chrM.bwa_aln.bam b/tests/input/empty.chrY_chrM.bwa_aln.SE.bam similarity index 100% rename from tests/input/empty.chrY_chrM.bwa_aln.bam rename to tests/input/empty.chrY_chrM.bwa_aln.SE.bam From 8860a825f476f59ec19910caa01388834d326320 Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Wed, 17 Sep 2025 16:27:23 -0400 Subject: [PATCH 12/15] Update README.md --- tests/input/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/input/README.md b/tests/input/README.md index 767507123..d4bbf554a 100644 --- a/tests/input/README.md +++ b/tests/input/README.md @@ -44,9 +44,9 @@ Combined beta values from `minfi` for two patient samples. The result of passing `empty.r[1,2].fq.gz` into STAR alignment. -## empty.chrY_chrM.bwa_aln.bam +## empty.chrY_chrM.bwa_aln.SE.bam -The result of passing `empty.r[1,2].fq.gz` into BWA aln alignment. +The result of passing `empty.r1.fq.gz` into BWA aln Single-End alignment. ## empty.r1.fq.gz From 2b409139e7a40d4b3b3afffb04f3f0af5a893fe8 Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Fri, 19 Sep 2025 10:01:45 -0400 Subject: [PATCH 13/15] Update .gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index dccc1afd1..c1ff16be3 100644 --- a/.gitignore +++ b/.gitignore @@ -5,6 +5,7 @@ /*.fa /*.gtf /*.bam +/*.bai /*.sam /*.log From 02fab9f7ab401852b63ce500d26d020876ac04ac Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Fri, 19 Sep 2025 10:12:28 -0400 Subject: [PATCH 14/15] ci: updates to latest --- .github/workflows/miniwdl-check.yaml | 2 +- .github/workflows/pull-check.yaml | 4 ++-- .github/workflows/sprocket-check.yaml | 5 +---- .github/workflows/sprocket-lint.yaml | 5 +---- .github/workflows/validate-inputs.yaml | 2 +- 5 files changed, 6 insertions(+), 12 deletions(-) diff --git a/.github/workflows/miniwdl-check.yaml b/.github/workflows/miniwdl-check.yaml index 14fa817bc..479ffc234 100644 --- a/.github/workflows/miniwdl-check.yaml +++ b/.github/workflows/miniwdl-check.yaml @@ -6,7 +6,7 @@ jobs: miniwdl_check: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python uses: actions/setup-python@v1 with: diff --git a/.github/workflows/pull-check.yaml b/.github/workflows/pull-check.yaml index 6e935017b..b8850b3c6 100644 --- a/.github/workflows/pull-check.yaml +++ b/.github/workflows/pull-check.yaml @@ -10,7 +10,7 @@ jobs: import_syntax_check: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Check import syntax run: | EXITCODE=0 @@ -41,7 +41,7 @@ jobs: docker_pull_check: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Ensure current SemVer'd docker images are being pulled run: | EXITCODE=0 diff --git a/.github/workflows/sprocket-check.yaml b/.github/workflows/sprocket-check.yaml index 6e480e19c..5338d9497 100644 --- a/.github/workflows/sprocket-check.yaml +++ b/.github/workflows/sprocket-check.yaml @@ -6,9 +6,6 @@ jobs: sprocket_check: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Run sprocket uses: stjude-rust-labs/sprocket-action@main - with: - deny-warnings: true - exclude-patterns: template diff --git a/.github/workflows/sprocket-lint.yaml b/.github/workflows/sprocket-lint.yaml index f809a2ecd..0b7f286e5 100644 --- a/.github/workflows/sprocket-lint.yaml +++ b/.github/workflows/sprocket-lint.yaml @@ -6,11 +6,8 @@ jobs: sprocket_lint: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Run sprocket uses: stjude-rust-labs/sprocket-action@main with: lint: true - deny-notes: true - except: ContainerUri - exclude-patterns: template diff --git a/.github/workflows/validate-inputs.yaml b/.github/workflows/validate-inputs.yaml index 80b42a84f..e645e5636 100644 --- a/.github/workflows/validate-inputs.yaml +++ b/.github/workflows/validate-inputs.yaml @@ -6,7 +6,7 @@ jobs: validate_inputs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Validate Reference Inputs uses: stjude-rust-labs/sprocket-action@main with: From 459a12f024cf14567fde19d021bd9b8146b007f7 Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Fri, 19 Sep 2025 11:32:39 -0400 Subject: [PATCH 15/15] Update sprocket.toml --- sprocket.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/sprocket.toml b/sprocket.toml index 41be8f773..b84f31f61 100644 --- a/sprocket.toml +++ b/sprocket.toml @@ -1,4 +1,5 @@ [check] +all_lint_rules = true except = ["ContainerUri"] deny_notes = true