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nf-core_modules/tests/modules/ascat/test.yml

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ASCAT (#1332) * First commit * putting correct links for singularity and docker containers (just had to search for bioconda+ascat to find them, and then put them in like the rest of the nf-core tools had it * adding first try of relevant commands (not working yet, just took their basic pipeline example * test commit * remove test * starting up work with module after 3.0.0 upgrade * add ascat.prepareHTS statemet * add location of docker for new mulled alleleCounter+ASCAT container * first full run with ASCAT on HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam * add notes on dropbox download * use a newer pytest_modules.yml * add outpit * trying to align with current Sarek output * adding in FH comments * busy clearing up arguments and testing. Still WIP * first working run, in nextflow, with sarek-like output. Still needs more work on input arguments * cleaning up before writing up findings * testing with putting in arguments in args * draft for solution 3 style for arguments * one more test added * adding FH map * finished testing maps for args * wrap-up cram/crai test successfully * updates to address ability to put in ref.fasta argument for cram running * adding remaining import-HTS commands in as args, and removing the chr21/chr22 only testing to test-nextflow.config * first test with auto-downloading the s3-data (when not given as an argument) * removing download-logic for supporting files, documenting in meta.yml, fixing ref_fasta bug * adding mulled singularity container * removing tests * fix left padding lint issue * lint failure in meta.yml * more linting errors * add when argument * adding stub functionality * add stub run * correct md5sum for versions.yml * more testing with -runstub * stub code in pure bash - not mixed with R * reformat version.yml * get rid of absolute paths in test.yml * correct wrong md5sum * adding allelecount conda link * rename normal_bam to input_bam etc * let the pipeline dev worry about matching the right loci and allele files * dont hardcode default genomebuild * adding download instruction comment * add doi * fix conda addition bug * add args documentation * test new indent * new test with meta.yml indentation * retry with new meta.yml * retry with new meta.yml - now with empty lines around * retry with new meta.yml - remove trailing whitepsace * trying to fix found quote character that cannot start any token error * try with one empty line above triple-quote and no empty line below * trying with pipe character * checking if its the ending triple quote * one more try with meta.yml * test update bioconda versioning for linting failure * test update bioconda versioning for linting failure 2 * testing allelecounter version error on conda Co-authored-by: @lassefolkersen Co-authored-by: @FriederikeHanssen
2022-03-15 10:18:43 +00:00
- name: ascat test_ascat
command: nextflow run tests/modules/ascat -entry test_ascat -c tests/config/nextflow.config -stub-run
tags:
- ascat
files:
Added output files to ASCAT (#1820) * add unzip alleles + loci * fix the partial absolute prefix path * exchanged deprecated function + added metrics * updated meta * tested logRCorrection + cram input * added BED for WES * added outputs + alleleCounter version * test samtools chr operations, fixed cancerit conda * ch formatting, fasta, bed input * comment out local tests * added metrics, bed, ref_fasta * rm print statement * added stub outputs * rm versions.yml * fix linting * rm fictitious md5sums for stub-run * try fixing top-level of stub versions.yml * ordered inputs alphabetically, ref_fasta -> fasta * rm R system command, adjust meta.yml * prettier yml * added outputs + prefix to outputs * added test-yml outputs * change underscores to dots
2022-06-28 12:45:57 +00:00
- path: output/ascat/test.after_correction.gc_rt.test.tumour.germline.png
- path: output/ascat/test.after_correction.gc_rt.test.tumour.tumour.png
- path: output/ascat/test.before_correction.test.tumour.germline.png
- path: output/ascat/test.before_correction.test.tumour.tumour.png
ASCAT (#1332) * First commit * putting correct links for singularity and docker containers (just had to search for bioconda+ascat to find them, and then put them in like the rest of the nf-core tools had it * adding first try of relevant commands (not working yet, just took their basic pipeline example * test commit * remove test * starting up work with module after 3.0.0 upgrade * add ascat.prepareHTS statemet * add location of docker for new mulled alleleCounter+ASCAT container * first full run with ASCAT on HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam * add notes on dropbox download * use a newer pytest_modules.yml * add outpit * trying to align with current Sarek output * adding in FH comments * busy clearing up arguments and testing. Still WIP * first working run, in nextflow, with sarek-like output. Still needs more work on input arguments * cleaning up before writing up findings * testing with putting in arguments in args * draft for solution 3 style for arguments * one more test added * adding FH map * finished testing maps for args * wrap-up cram/crai test successfully * updates to address ability to put in ref.fasta argument for cram running * adding remaining import-HTS commands in as args, and removing the chr21/chr22 only testing to test-nextflow.config * first test with auto-downloading the s3-data (when not given as an argument) * removing download-logic for supporting files, documenting in meta.yml, fixing ref_fasta bug * adding mulled singularity container * removing tests * fix left padding lint issue * lint failure in meta.yml * more linting errors * add when argument * adding stub functionality * add stub run * correct md5sum for versions.yml * more testing with -runstub * stub code in pure bash - not mixed with R * reformat version.yml * get rid of absolute paths in test.yml * correct wrong md5sum * adding allelecount conda link * rename normal_bam to input_bam etc * let the pipeline dev worry about matching the right loci and allele files * dont hardcode default genomebuild * adding download instruction comment * add doi * fix conda addition bug * add args documentation * test new indent * new test with meta.yml indentation * retry with new meta.yml * retry with new meta.yml - now with empty lines around * retry with new meta.yml - remove trailing whitepsace * trying to fix found quote character that cannot start any token error * try with one empty line above triple-quote and no empty line below * trying with pipe character * checking if its the ending triple quote * one more try with meta.yml * test update bioconda versioning for linting failure * test update bioconda versioning for linting failure 2 * testing allelecounter version error on conda Co-authored-by: @lassefolkersen Co-authored-by: @FriederikeHanssen
2022-03-15 10:18:43 +00:00
- path: output/ascat/test.cnvs.txt
Added output files to ASCAT (#1820) * add unzip alleles + loci * fix the partial absolute prefix path * exchanged deprecated function + added metrics * updated meta * tested logRCorrection + cram input * added BED for WES * added outputs + alleleCounter version * test samtools chr operations, fixed cancerit conda * ch formatting, fasta, bed input * comment out local tests * added metrics, bed, ref_fasta * rm print statement * added stub outputs * rm versions.yml * fix linting * rm fictitious md5sums for stub-run * try fixing top-level of stub versions.yml * ordered inputs alphabetically, ref_fasta -> fasta * rm R system command, adjust meta.yml * prettier yml * added outputs + prefix to outputs * added test-yml outputs * change underscores to dots
2022-06-28 12:45:57 +00:00
- path: output/ascat/test.metrics.txt
- path: output/ascat/test.normal_alleleFrequencies_chr21.txt
- path: output/ascat/test.normal_alleleFrequencies_chr22.txt
ASCAT (#1332) * First commit * putting correct links for singularity and docker containers (just had to search for bioconda+ascat to find them, and then put them in like the rest of the nf-core tools had it * adding first try of relevant commands (not working yet, just took their basic pipeline example * test commit * remove test * starting up work with module after 3.0.0 upgrade * add ascat.prepareHTS statemet * add location of docker for new mulled alleleCounter+ASCAT container * first full run with ASCAT on HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam * add notes on dropbox download * use a newer pytest_modules.yml * add outpit * trying to align with current Sarek output * adding in FH comments * busy clearing up arguments and testing. Still WIP * first working run, in nextflow, with sarek-like output. Still needs more work on input arguments * cleaning up before writing up findings * testing with putting in arguments in args * draft for solution 3 style for arguments * one more test added * adding FH map * finished testing maps for args * wrap-up cram/crai test successfully * updates to address ability to put in ref.fasta argument for cram running * adding remaining import-HTS commands in as args, and removing the chr21/chr22 only testing to test-nextflow.config * first test with auto-downloading the s3-data (when not given as an argument) * removing download-logic for supporting files, documenting in meta.yml, fixing ref_fasta bug * adding mulled singularity container * removing tests * fix left padding lint issue * lint failure in meta.yml * more linting errors * add when argument * adding stub functionality * add stub run * correct md5sum for versions.yml * more testing with -runstub * stub code in pure bash - not mixed with R * reformat version.yml * get rid of absolute paths in test.yml * correct wrong md5sum * adding allelecount conda link * rename normal_bam to input_bam etc * let the pipeline dev worry about matching the right loci and allele files * dont hardcode default genomebuild * adding download instruction comment * add doi * fix conda addition bug * add args documentation * test new indent * new test with meta.yml indentation * retry with new meta.yml * retry with new meta.yml - now with empty lines around * retry with new meta.yml - remove trailing whitepsace * trying to fix found quote character that cannot start any token error * try with one empty line above triple-quote and no empty line below * trying with pipe character * checking if its the ending triple quote * one more try with meta.yml * test update bioconda versioning for linting failure * test update bioconda versioning for linting failure 2 * testing allelecounter version error on conda Co-authored-by: @lassefolkersen Co-authored-by: @FriederikeHanssen
2022-03-15 10:18:43 +00:00
- path: output/ascat/test.purityploidy.txt
- path: output/ascat/test.segments.txt
Added output files to ASCAT (#1820) * add unzip alleles + loci * fix the partial absolute prefix path * exchanged deprecated function + added metrics * updated meta * tested logRCorrection + cram input * added BED for WES * added outputs + alleleCounter version * test samtools chr operations, fixed cancerit conda * ch formatting, fasta, bed input * comment out local tests * added metrics, bed, ref_fasta * rm print statement * added stub outputs * rm versions.yml * fix linting * rm fictitious md5sums for stub-run * try fixing top-level of stub versions.yml * ordered inputs alphabetically, ref_fasta -> fasta * rm R system command, adjust meta.yml * prettier yml * added outputs + prefix to outputs * added test-yml outputs * change underscores to dots
2022-06-28 12:45:57 +00:00
- path: output/ascat/test.tumour.ASPCF.png
- path: output/ascat/test.tumour.sunrise.png
- path: output/ascat/test.tumour_alleleFrequencies_chr21.txt
- path: output/ascat/test.tumour_alleleFrequencies_chr22.txt
- path: output/ascat/test.tumour_normalBAF.txt
- path: output/ascat/test.tumour_normalLogR.txt
- path: output/ascat/test.tumour_tumourBAF.txt
- path: output/ascat/test.tumour_tumourLogR.txt
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