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nf-core_modules/tests/modules/ascat/main.nf

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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 06:18:43 -04:00
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
Update ASCAT module (#1805) * 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
2022-06-23 11:06:00 -04:00
include { ASCAT as ASCAT_SIMPLE } from '../../../modules/ascat/main.nf'
include { ASCAT as ASCAT_PLOIDY_AND_PURITY } from '../../../modules/ascat/main.nf'
include { ASCAT as ASCAT_CRAM } from '../../../modules/ascat/main.nf'
include { UNZIP as UNZIP_ALLELES } from '../../../modules/unzip/main.nf'
include { UNZIP as UNZIP_LOCI } from '../../../modules/unzip/main.nf'
include { UNZIP as UNZIP_GC } from '../../../modules/unzip/main.nf'
include { UNZIP as UNZIP_RT } from '../../../modules/unzip/main.nf'
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 06:18:43 -04:00
workflow test_ascat {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
]
Update ASCAT module (#1805) * 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
2022-06-23 11:06:00 -04:00
ASCAT_SIMPLE ( input , [], [], [], [], [], [])
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 06:18:43 -04:00
}
Update ASCAT module (#1805) * 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
2022-06-23 11:06:00 -04:00
// extended tests running with 1000 genomes data. Data is downloaded as follows:
// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai
// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00155/alignment/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00155/alignment/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai
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 06:18:43 -04:00
Update ASCAT module (#1805) * 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
2022-06-23 11:06:00 -04:00
// workflow test_ascat_with_ploidy_and_purity {
// input = [ [ id:'test', single_end:false ], // meta map
// file("/mnt/volume/ascat/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam", checkIfExists: true),
// file("/mnt/volume/ascat/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai", checkIfExists: true),
// file("/mnt/volume/ascat/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam", checkIfExists: true),
// file("/mnt/volume/ascat/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai", checkIfExists: true)
// ]
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 06:18:43 -04:00
Update ASCAT module (#1805) * 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
2022-06-23 11:06:00 -04:00
// allele_path = file("/mnt/volume/repos/modules/test_ascat2/G1000_alleles_hg19.zip", checkIfExists: true)
// allele_files = [[ id: allele_path.BaseName ], allele_path ]
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 06:18:43 -04:00
Update ASCAT module (#1805) * 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
2022-06-23 11:06:00 -04:00
// loci_path = file("/mnt/volume/repos/modules/test_ascat2/G1000_loci_hg19.zip", checkIfExists: true)
// loci_files = [[ id: loci_path.BaseName ], loci_path ]
// gc_path = file("/mnt/volume/repos/modules/test_ascat2/GC_G1000_hg19.zip", checkIfExists: true)
// gc_file = [[ id: gc_path.BaseName ], gc_path ]
// rt_path = file("/mnt/volume/repos/modules/test_ascat2/RT_G1000_hg19.zip", checkIfExists: true)
// rt_file = [[ id: rt_path.BaseName ], rt_path ]
// UNZIP_ALLELES(allele_files)
// UNZIP_LOCI(loci_files)
// UNZIP_GC(gc_file)
// ASCAT_PLOIDY_AND_PURITY ( input ,
// UNZIP_ALLELES.out.unzipped_archive.map{ it[1] },
// UNZIP_LOCI.out.unzipped_archive.map{ it[1] },
// [], // optional bed_file for WES
// [], // optional fasta
// UNZIP_GC.out.unzipped_archive.map{ it[1] }, // optional GC_correction
// []) // optional RT_correction
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 06:18:43 -04:00
//
Update ASCAT module (#1805) * 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
2022-06-23 11:06:00 -04:00
// }
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 06:18:43 -04:00
// extended tests running with 1000 genomes data. Data is downloaded as follows:
// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00145/alignment/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai
// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00145/alignment/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram
// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00146/alignment/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai
// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00146/alignment/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram
Update ASCAT module (#1805) * 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
2022-06-23 11:06:00 -04:00
// workflow test_ascat_with_crams {
// input = [
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 06:18:43 -04:00
// [ id:'test', single_end:false ], // meta map
Update ASCAT module (#1805) * 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
2022-06-23 11:06:00 -04:00
// file("/mnt/volume/ascat/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram", checkIfExists: true),
// file("/mnt/volume/ascat/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai", checkIfExists: true),
// file("/mnt/volume/ascat/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram", checkIfExists: true),
// file("/mnt/volume/ascat/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai", checkIfExists: true)
// ]
// allele_path = file("/mnt/volume/repos/modules/test_ascat2/G1000_alleles_hg19.zip", checkIfExists: true)
// allele_files = [[ id: allele_path.BaseName ], allele_path ]
// loci_path = file("/mnt/volume/repos/modules/test_ascat2/G1000_loci_hg19.zip", checkIfExists: true)
// loci_files = [[ id: loci_path.BaseName ], loci_path ]
// gc_path = file("/mnt/volume/repos/modules/test_ascat2/GC_G1000_hg19.zip", checkIfExists: true)
// gc_file = [[ id: gc_path.BaseName ], gc_path ]
// rt_path = file("/mnt/volume/repos/modules/test_ascat2/RT_G1000_hg19.zip", checkIfExists: true)
// rt_file = [[ id: rt_path.BaseName ], rt_path ]
// fasta = file("/mnt/volume/ascat/human_g1k_v37.fasta", checkIfExists: true)
// UNZIP_ALLELES(allele_files)
// UNZIP_LOCI(loci_files)
// UNZIP_GC(gc_file)
// UNZIP_RT(rt_file)
// ASCAT_CRAM ( input ,
// UNZIP_ALLELES.out.unzipped_archive.map{ it[1] },
// UNZIP_LOCI.out.unzipped_archive.map{ it[1] },
// [],
// fasta,
// UNZIP_GC.out.unzipped_archive.map{ it[1] },
// UNZIP_RT.out.unzipped_archive.map{ it[1] })
// }
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 06:18:43 -04:00
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