Skip to content

Commit

Permalink
Remove bam files
Browse files Browse the repository at this point in the history
  • Loading branch information
edmundmiller committed Dec 16, 2024
1 parent 226bae6 commit ba256f1
Show file tree
Hide file tree
Showing 8 changed files with 98 additions and 39 deletions.
81 changes: 81 additions & 0 deletions .nf-test.log
Original file line number Diff line number Diff line change
@@ -0,0 +1,81 @@
Dec-16 02:15:48.643 [main] INFO com.askimed.nf.test.App - nf-test 0.9.2
Dec-16 02:15:48.667 [main] INFO com.askimed.nf.test.App - Arguments: [test, --update-snapshot, --wipe-snapshot, --profile, +docker, workflows/tests/aligner/bowtie2.nf.test, workflows/tests/aligner/bwamem2.nf.test, workflows/tests/aligner/bwa.nf.test, workflows/tests/aligner/dragmap.nf.test, workflows/tests/aligner/hisat2.nf.test, workflows/tests/aligner/star.nf.test]
Dec-16 02:15:49.565 [main] INFO com.askimed.nf.test.App - Nextflow Version: 24.10.2
Dec-16 02:15:49.566 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Load config from file /workspace/nascent/nf-test.config...
Dec-16 02:15:50.382 [main] WARN com.askimed.nf.test.nextflow.NextflowScript - Module /workspace/nascent/subworkflows/local/dreg_prep/main.nf: Dependency '/workspace/nascent/subworkflows/local/dreg_prep/../modules/nf-core/bedtools/bamtobed/main.nf' not found.
Dec-16 02:15:50.412 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 230 files from directory /workspace/nascent in 0.386 sec
Dec-16 02:15:50.415 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 6 files containing tests.
Dec-16 02:15:50.415 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found files: [/workspace/nascent/workflows/tests/aligner/dragmap.nf.test, /workspace/nascent/workflows/tests/aligner/bwa.nf.test, /workspace/nascent/workflows/tests/aligner/star.nf.test, /workspace/nascent/workflows/tests/aligner/bowtie2.nf.test, /workspace/nascent/workflows/tests/aligner/hisat2.nf.test, /workspace/nascent/workflows/tests/aligner/bwamem2.nf.test]
Dec-16 02:15:51.025 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Found 9 tests to execute.
Dec-16 02:15:51.026 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan
Dec-16 02:15:51.026 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Bowtie2' from file '/workspace/nascent/workflows/tests/aligner/bowtie2.nf.test'.
Dec-16 02:15:51.026 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'e3410fa6: Should run with defaults'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
Dec-16 02:18:37.490 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/workspace/nascent/workflows/tests/aligner/bowtie2.nf.test.snap'
Dec-16 02:18:37.673 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run with defaults' do not match. Update snapshots flag set.
Dec-16 02:18:37.673 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'Should run with defaults'
Dec-16 02:18:37.748 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/bowtie2.nf.test.snap'
Dec-16 02:18:37.749 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'e3410fa6: Should run with defaults' finished. status: PASSED
Dec-16 02:18:37.752 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Clean up obsolete snapshots
Dec-16 02:18:37.809 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/bowtie2.nf.test.snap'
Dec-16 02:18:37.809 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Bowtie2' finished. snapshot file: true, skipped tests: false, failed tests: false
Dec-16 02:18:37.812 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'BWA' from file '/workspace/nascent/workflows/tests/aligner/bwa.nf.test'.
Dec-16 02:18:37.812 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'e912cd0f: Should run with defaults'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
Dec-16 02:22:23.045 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/workspace/nascent/workflows/tests/aligner/bwa.nf.test.snap'
Dec-16 02:22:23.366 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run with defaults' do not match. Update snapshots flag set.
Dec-16 02:22:23.367 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'Should run with defaults'
Dec-16 02:22:23.501 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/bwa.nf.test.snap'
Dec-16 02:22:23.501 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'e912cd0f: Should run with defaults' finished. status: PASSED
Dec-16 02:22:23.502 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'ca549b93: Should work with BWA Index'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
Dec-16 02:24:03.940 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should work with BWA Index' match.
Dec-16 02:24:03.940 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'ca549b93: Should work with BWA Index' finished. status: PASSED
Dec-16 02:24:03.941 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '71a06a5b: Should work with gzipped references'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
Dec-16 02:25:20.210 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should work with gzipped references' match.
Dec-16 02:25:20.211 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '71a06a5b: Should work with gzipped references' finished. status: PASSED
Dec-16 02:25:20.211 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Clean up obsolete snapshots
Dec-16 02:25:20.664 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/bwa.nf.test.snap'
Dec-16 02:25:20.664 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'BWA' finished. snapshot file: true, skipped tests: false, failed tests: false
Dec-16 02:25:20.666 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'bwamem2' from file '/workspace/nascent/workflows/tests/aligner/bwamem2.nf.test'.
Dec-16 02:25:20.666 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '40528c2d: Should run with defaults'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
Dec-16 02:27:44.578 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/workspace/nascent/workflows/tests/aligner/bwamem2.nf.test.snap'
Dec-16 02:27:44.713 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run with defaults' do not match. Update snapshots flag set.
Dec-16 02:27:44.713 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'Should run with defaults'
Dec-16 02:27:44.920 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/bwamem2.nf.test.snap'
Dec-16 02:27:44.920 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '40528c2d: Should run with defaults' finished. status: PASSED
Dec-16 02:27:44.921 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Clean up obsolete snapshots
Dec-16 02:27:45.186 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/bwamem2.nf.test.snap'
Dec-16 02:27:45.186 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'bwamem2' finished. snapshot file: true, skipped tests: false, failed tests: false
Dec-16 02:27:45.186 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'DRAGMAP' from file '/workspace/nascent/workflows/tests/aligner/dragmap.nf.test'.
Dec-16 02:27:45.186 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'e16b50e4: Should run with defaults'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
Dec-16 02:31:00.293 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/workspace/nascent/workflows/tests/aligner/dragmap.nf.test.snap'
Dec-16 02:31:00.427 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run with defaults' do not match. Update snapshots flag set.
Dec-16 02:31:00.428 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'Should run with defaults'
Dec-16 02:31:00.502 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/dragmap.nf.test.snap'
Dec-16 02:31:00.502 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'e16b50e4: Should run with defaults' finished. status: PASSED
Dec-16 02:31:00.503 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Clean up obsolete snapshots
Dec-16 02:31:00.610 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/dragmap.nf.test.snap'
Dec-16 02:31:00.610 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'DRAGMAP' finished. snapshot file: true, skipped tests: false, failed tests: false
Dec-16 02:31:00.611 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'HISAT2' from file '/workspace/nascent/workflows/tests/aligner/hisat2.nf.test'.
Dec-16 02:31:00.611 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '54f5dffc: Should run with defaults'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
Dec-16 02:34:03.031 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/workspace/nascent/workflows/tests/aligner/hisat2.nf.test.snap'
Dec-16 02:34:03.729 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run with defaults' do not match. Update snapshots flag set.
Dec-16 02:34:03.729 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'Should run with defaults'
Dec-16 02:34:04.295 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/hisat2.nf.test.snap'
Dec-16 02:34:04.296 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '54f5dffc: Should run with defaults' finished. status: PASSED
Dec-16 02:34:04.296 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Clean up obsolete snapshots
Dec-16 02:34:04.846 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/hisat2.nf.test.snap'
Dec-16 02:34:04.846 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'HISAT2' finished. snapshot file: true, skipped tests: false, failed tests: false
Dec-16 02:34:04.846 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'STAR' from file '/workspace/nascent/workflows/tests/aligner/star.nf.test'.
Dec-16 02:34:04.846 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '32b4754c: Should run with defaults'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
Dec-16 02:38:34.918 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/workspace/nascent/workflows/tests/aligner/star.nf.test.snap'
Dec-16 02:38:39.215 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run with defaults' do not match. Update snapshots flag set.
Dec-16 02:38:39.216 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'Should run with defaults'
Dec-16 02:38:42.370 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/star.nf.test.snap'
Dec-16 02:38:42.370 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '32b4754c: Should run with defaults' finished. status: PASSED
Dec-16 02:38:42.370 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '99482460: Should run with gzipped gtf'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
Dec-16 02:42:52.588 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'gzip_software_versions' match.
Dec-16 02:42:52.589 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run with gzipped gtf' match.
Dec-16 02:42:52.589 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '99482460: Should run with gzipped gtf' finished. status: PASSED
Dec-16 02:42:52.590 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Clean up obsolete snapshots
Dec-16 02:42:57.042 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/star.nf.test.snap'
Dec-16 02:42:57.042 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'STAR' finished. snapshot file: true, skipped tests: false, failed tests: false
Dec-16 02:42:57.043 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 9 tests. 0 tests failed. Done!
2 changes: 1 addition & 1 deletion tests/.nftignore
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ pipeline_info/*.{html,json,txt,yml}
**/*.command.log
**/*.bedGraph.gz
**/tagInfo.txt
**/*.bam
**/*.{bam,bai}
**/*.featureCounts.txt
**/*.featureCounts.txt.summary
**/DupRate_plot.pdf
Expand Down
5 changes: 1 addition & 4 deletions workflows/tests/aligner/bowtie2.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -384,9 +384,6 @@
"transcript_identification/intersect/jurkat_intersect.bed"
],
[
"cd4_REP1.sorted.bam.bai:md5,51c403cb04b2c69c35a67633649fab22",
"cd4_REP2.sorted.bam.bai:md5,57b08e29238c9fe070a00ec9658d975c",
"jurkat.sorted.bam.bai:md5,9fad0729e271deb77c8b67cb6578b0ff",
"cd4_REP1.sorted.bam.flagstat:md5,14e684e73cb41155ab1168a0a99a97e6",
"cd4_REP1.sorted.bam.idxstats:md5,e32ac3215ba948bb7dd1559dab6c3c36",
"cd4_REP1.sorted.bam.stats:md5,490f84b5520b83daa95653671ce43921",
Expand Down Expand Up @@ -438,6 +435,6 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-16T00:37:45.153123266"
"timestamp": "2024-12-16T02:18:37.673464926"
}
}
8 changes: 1 addition & 7 deletions workflows/tests/aligner/bwa.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -495,12 +495,6 @@
],
[
"cd4_intersect.saf:md5,635fcd8e2c060dc75db25564c2a664dc",
"cd4_REP1.sorted.bam.bai:md5,89c4319f5f28020940ba31ca7e602e84",
"cd4_REP2.sorted.bam.bai:md5,f87fb585bc0d570a16d5ae9230f36113",
"cd4_REP3.sorted.bam.bai:md5,39c4c10e041e812be47b20996c004594",
"cd4_REP4.sorted.bam.bai:md5,8cb9c3c74faf7c3594bdbd9fd642434d",
"jurkat_REP1.sorted.bam.bai:md5,78490e10f957ad2b0b05d1106e67d3d5",
"jurkat_REP2.sorted.bam.bai:md5,eff0f3690baa030685f76a0687301827",
"cd4_REP1.sorted.bam.flagstat:md5,863e2d506d5cc4239af98a5f31bbc906",
"cd4_REP1.sorted.bam.idxstats:md5,b1dd8bcbd23c53c21f0e11082d9315f2",
"cd4_REP1.sorted.bam.stats:md5,1536c80bae78b2062508e1de210f6387",
Expand Down Expand Up @@ -594,6 +588,6 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-16T00:42:17.554030501"
"timestamp": "2024-12-16T02:22:23.367403695"
}
}
5 changes: 1 addition & 4 deletions workflows/tests/aligner/bwamem2.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -412,9 +412,6 @@
],
[
"cd4_intersect.saf:md5,2528ed58898f6e1f9d3d54fc1381c4c6",
"cd4_REP1.sorted.bam.bai:md5,941ed9d1bf8e04ab916967a4f6c03db4",
"cd4_REP2.sorted.bam.bai:md5,a89d7777e8172df5a13872061f358ee6",
"jurkat.sorted.bam.bai:md5,2f011fbac6305bd573b339e926efd1ed",
"cd4_REP1.sorted.bam.flagstat:md5,863e2d506d5cc4239af98a5f31bbc906",
"cd4_REP1.sorted.bam.idxstats:md5,b1dd8bcbd23c53c21f0e11082d9315f2",
"cd4_REP1.sorted.bam.stats:md5,1536c80bae78b2062508e1de210f6387",
Expand Down Expand Up @@ -472,6 +469,6 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-16T00:48:07.304023197"
"timestamp": "2024-12-16T02:27:44.713604463"
}
}
5 changes: 1 addition & 4 deletions workflows/tests/aligner/dragmap.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -434,9 +434,6 @@
"jurkat.minus.bigWig:md5,22daac83d393dcca8f1cc96580d3d4f3",
"jurkat.plus.bedGraph:md5,ddabf19e2172df4b80b7ce434035403e",
"jurkat.plus.bigWig:md5,ca73f44638c066f25261efffa1eedc7f",
"cd4_REP1.sorted.bam.bai:md5,2216ef93d05d9a40bd46060a31eb55b0",
"cd4_REP2.sorted.bam.bai:md5,bf9b9351dc55e484e0f514ee757fd5bd",
"jurkat.sorted.bam.bai:md5,81404074238d45c530ad19cc2007f23a",
"cd4_REP1.sorted.bam.flagstat:md5,6a27aa41830e5f10a2c54c8a05611f9a",
"cd4_REP1.sorted.bam.idxstats:md5,75eaf648cea73812913344af3851ce16",
"cd4_REP1.sorted.bam.stats:md5,80bfe47bc5be703b51313a4b2fbcc57f",
Expand Down Expand Up @@ -477,6 +474,6 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-16T00:51:02.590820921"
"timestamp": "2024-12-16T02:31:00.42810535"
}
}
5 changes: 1 addition & 4 deletions workflows/tests/aligner/hisat2.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -432,9 +432,6 @@
"jurkat.minus.bigWig:md5,8a0ca6db6626d3fefb518f0d35dd1abc",
"jurkat.plus.bedGraph:md5,835edbd98f6d5d69e56de05e1a837b7c",
"jurkat.plus.bigWig:md5,66e82005e6c6730e970f7506bf93325c",
"cd4_REP1.sorted.bam.bai:md5,f0cb418bf72d86f4f12d6a8eadeba3d7",
"cd4_REP2.sorted.bam.bai:md5,a3bb5408bd4aad1d84205928be54d255",
"jurkat.sorted.bam.bai:md5,808b536f2007f219e467803af5f5d6e4",
"cd4_REP1.sorted.bam.flagstat:md5,aa26d19a689b2fe97e254f125e1f7bcb",
"cd4_REP1.sorted.bam.idxstats:md5,d523e6e25ce8659871df4104dab503b0",
"cd4_REP1.sorted.bam.stats:md5,57b98494241870644c74edda7d503232",
Expand Down Expand Up @@ -483,6 +480,6 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-16T00:53:08.096831952"
"timestamp": "2024-12-16T02:34:03.729876999"
}
}
Loading

0 comments on commit ba256f1

Please sign in to comment.