diff --git a/modules/pbccs/main.nf b/modules/pbccs/main.nf index 7e70ac14..55eacd76 100644 --- a/modules/pbccs/main.nf +++ b/modules/pbccs/main.nf @@ -37,9 +37,9 @@ process PBCCS { ccs \\ $bam \\ ${prefix}.chunk${chunk_num}.bam \\ - --report-file ${prefix}.report.txt \\ - --report-json ${prefix}.report.json \\ - --metrics-json ${prefix}.metrics.json.gz \\ + --report-file ${prefix}.chunk${chunk_num}.report.txt \\ + --report-json ${prefix}.chunk${chunk_num}.report.json \\ + --metrics-json ${prefix}.chunk${chunk_num}.metrics.json.gz \\ --chunk $chunk_num/$chunk_on \\ -j $task.cpus \\ $options.args diff --git a/modules/pbccs/meta.yml b/modules/pbccs/meta.yml index 38f31496..f55c0d71 100644 --- a/modules/pbccs/meta.yml +++ b/modules/pbccs/meta.yml @@ -42,10 +42,26 @@ output: type: file description: File containing software versions pattern: "versions.yml" - - css: + - bam: type: file - description: Consensus sequences - pattern: "*.ccs.bam" + description: CCS sequences in bam format + pattern: "*.bam" + - pbi: + type: file + description: PacBio Index of CCS sequences + pattern: "*.pbi" + - report_txt: + type: file + description: Summary of CCS in txt format + pattern: ".txt" + - report_json: + type: file + description: Summary of CCS in txt json + pattern: ".json" + - metrics: + type: file + description: Metrics about zmws + pattern: "*.json.gz" authors: - "@sguizard" diff --git a/tests/__pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc b/tests/__pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc new file mode 100644 index 00000000..33acb836 Binary files /dev/null and b/tests/__pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc differ diff --git a/tests/modules/pbccs/test.yml b/tests/modules/pbccs/test.yml index 1d1651c4..af225eb1 100644 --- a/tests/modules/pbccs/test.yml +++ b/tests/modules/pbccs/test.yml @@ -4,12 +4,12 @@ - pbccs files: - path: output/pbccs/alz.chunk2.bam - md5sum: d1a0266d5df64b74409a21981071a1c6 + md5sum: 2b6451f2d0454eb08359cb84e2e4069c - path: output/pbccs/alz.chunk2.bam.pbi - md5sum: 582a4500ddcb3f4a24a443192620d039 - - path: output/pbccs/alz.metrics.json.gz + md5sum: 3112cda9744e3facbf38245d41aaf080 + - path: output/pbccs/alz.chunk2.metrics.json.gz contains: [ 'zmws' ] - - path: output/pbccs/alz.report.json + - path: output/pbccs/alz.chunk2.report.json contains: [ 'Created by pbcopper' ] - - path: output/pbccs/alz.report.txt + - path: output/pbccs/alz.chunk2.report.txt md5sum: bbc5bd7a1269345cf7a7f3d4c746024b