Adds bwa -k 23 and GenomeChronicler as tool #16
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cgpu
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Jan 10, 2020
cgpu
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- Adds -k 23 (bwa mem seed length)
- Exposes as params bwa_cpus, sort_cpus
- Adds GenomeChronicler in tools (sarek logic)
- [x] Adds -k 23 (bwa mem seed length) - [x] Exposes as params bwa_cpus, sort_cpus - [x] Adds GenomeChronicler in tools (sarek logic)
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Jan 13, 2020
* nf-core bump-version . 2.5.1dev * Remove PublishDirMode from test profile (nf-core#40) * remove PublishDirMode from test profile * update all tools * minor updates + typo fix (nf-core#42) * minor updates + typo fix * fix VEP automated builds * add location for abstracts * remove reference to old buil.nf script * update CHANGELOG * Update docs/reference.md Co-Authored-By: Szilveszter Juhos <szilveszter.juhos@scilifelab.se> * Update docs/reference.md * Update docs/reference.md * Worfklow (nf-core#45) * Add workflow figure * Include workflow figure in readme * Update CHANGELOG * add minimal genome and update some processes * Start adding mouse data * Update iGenomes.config * Add tbi * Drop ASCAT files * apply changes from 2.5.1 to dev * bump version to 2.5.2dev * update CHANGELOG * update tiddit to 2.8.1 * Use Version 98 of Mouse * Add for grcm38 * Adjust mus musculus DB * Annotation * add smallerGRCh37 and minimalGRCh37 * use bwa aln when no knowIndels, otherwise use bwa mem, noIntervals currently in the process of being added everywhere * don't use bwa aln * add automatic generation of intervals file based on fastaFai file * Adjusted genomes.config * Should be list * Set genomes_base to something * Revert back * enable CreateIntervalsBed for intervals_list from GATK Bundle * Add proper calling list * Use the bed file * remove temp file * update CHANGELOG * Fix genome fa.fai * Add in mgpv5 * Try short track * Add in species handling * Document new parameter species * Add changelog * Fix iGenomes stuff * Add in note about GRCm38 * Fix small fai index issue * Adjusted quotes in genomes.config * And the same for igenomes * Better folder structure for Mouse Genome Project data * Minor adjustment to propoer paths * Apply suggestions from code review Add changes by Maxime Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com> * Remove space * Move it up * Update CHANGELOG.md Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com> * add minimal tests * fix processes with no intervals * add comments * params noIntervals -> no_intervals * sort genomes + add news * code polishing * update CHANGELOG * add split_fastq params to split the fastq files with the splitFastq() nf method * add tests * temporarely remove TIDDIT tests * add sention for bwa mem * disable docker and singularity * disable container * add fastaFai for bwamem * remove module samtools from label sentieon * fix output from bwa mem * fix output channel BamMapped from MapReads * set params.sentieon to null by default * add SentieonDedup process * fix typo * add fastaFai to SentieonDedup process * fix bam indexing * fix bam indexing * fix bam indexing * add SentieonBQSR * add label sentieon to SentieonBQSR * fix metrics output for SentieonBQSR * increase cpus for Sentieon BQSR * remove indexing * add index for dedup * bwa mem sentieon specific process * TSV file for sentieon Dedup * TSV for every step for Sentieon * recal -> deduped * fix input for TSV recalibrate * enable restart from recalibrate with TSV with Sentieon * fix sention variant calling from mapping and recalibrate * code polishing * add dump tag for imput sample * add dump tag for bamDedupedSentieon * code polishing * code polishing * code polishing * code polishing * remove when statement * fix typo * remove tsv for recalibrate with sentieon * add dnascope dnaseq * fix dnascope * add TNscope process * fix TNscope output * add pon for TNscope * add params.pon_index * add annotation for sention DNAseq, DNAscope, TNscope * add default pon_index * typo * fix typo * improve automatic annotation * typo * typo * add condition on when statement on TNscope * clean up * code polish * add CODEOWNERS file * add when statement on all sentieon processes with params.sentieon * remove munin sentieon specific configs from config * load sarek specific config * update path to specific config * update docs * remove Freebayes * update workflow image * remove old logo * fix tests * add docs about params split_fastq * update CHANGELOG * improve docs * more tests but less NF versions * actually run the tests * typo * simplify configs * add test for mpileup * go crazy with tests * fix tests * includ test.config * restore FreeBayes * remove label memory_max from BaseRecalibrator process to fix nf-core#72 * add --skipQC all and --tools Manta,mpileup,Strelka to minimal genome tests * update Nextflow version * update Nextflow version * update Nextflow * add --step annotation to profile * don't need to specify step here * move params initalization * add docs * fix markdownlint * more complete docs + sort genomes * improve tests * update docs * update CHANGELOG * improve script * fix tests * better comments * better comments * fix error on channel name * fix output for MergeBamRecal * fix MergeBamRecal output * fix TSV file * update comments and docs * add warning for sentieon only processes * nf-core bump-version . 2.5.2 * manual bump-version . 2.5.2 * update workflow image * downgrade tools for release * update CHANGELOG * clean up and update workflow image * allow a * fix workflow image * Apply suggestions from code review * Apply suggestions from code review * Update docs/output.md * Apply suggestions from code review * Apply suggestions from code review * Apply suggestions from code review * Reformats `bwa mem | samtools sort` command; WIP suboptimal resource usage * Addresses #5 ;WIP * Removes max_ resource alloc labels from MarkDuplicatesSpark * Replaces .md.bam.bai->.md.bai (same as nf-core) * Add ${markdup_java_options} to MarkDuplicatesSpark (same as nf-core MarkDuplicates) * Changes MarkDuplicates --verbosity, DEBUG->INFO * Changes intervalBed.simpleName->intervalBed.baseName; nf-cored * Removes label cpus_1 from BaseRecalibratorSpark * Remove cpus_2 labels from ApplyBQSRSpark; DEBUG->INFO * Changes pseudo file "no_vepFile.txt" from https to s3 link * Removes java options from ApplyBQSRSpark * Removes java options from MarkDupesSpark * Add java-options to MarkDupesSpark; verbosity INFO->ERROR * Fixes dupe --java-options; 🤦 * Attempt to fix MarkDupesSpark; "--lower-case"->"-CAP"; Removed tmp * Adds soft-coded allocation of resources to MapReads * Initialise params for MapReads split resource alloc * Adds neglected curlies around params * Adds neglected \ to bash vars * Adds neglected \ to bash vars * WIP; MapReads optimisations * Implement resource alloc between bwa and samtools * Adds max, med soft coded resource alloc * Re-labels processes (from hard coded resources to soft) * Adds extra curlies to addrees priority of eval * Add explicit declaration of maxForks/process * Update med resource allocation function * Add echo true and echo of ${bwa_cpus} and ${sort_cpus} * Hard code heap in MarkDuplicatesSpark at 8g * Correct expected output bai in MarkDupes * Removes Spark versions; Not stable with low resources * Removes sorting; Picard might sort? * Do not assume sorting in MarkDupes * Adds explicit --ASSUME_SORT_ORDER unsorted * Adds missing \\ * Omits -k 23 * Bringing sorted back * Eliminating pipes in mapping step * Adds bwa -k 23 and GenomeChronicler as tool (cgpu#16) - [x] Adds -k 23 (bwa mem seed length) - [x] Exposes as params bwa_cpus, sort_cpus - [x] Adds GenomeChronicler in tools (sarek logic) Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com> Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Szilveszter Juhos <szilveszter.juhos@scilifelab.se>
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cgpu
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Jan 15, 2020
* nf-core bump-version . 2.5.1dev * Remove PublishDirMode from test profile (nf-core#40) * remove PublishDirMode from test profile * update all tools * minor updates + typo fix (nf-core#42) * minor updates + typo fix * fix VEP automated builds * add location for abstracts * remove reference to old buil.nf script * update CHANGELOG * Update docs/reference.md Co-Authored-By: Szilveszter Juhos <szilveszter.juhos@scilifelab.se> * Update docs/reference.md * Update docs/reference.md * Worfklow (nf-core#45) * Add workflow figure * Include workflow figure in readme * Update CHANGELOG * add minimal genome and update some processes * Start adding mouse data * Update iGenomes.config * Add tbi * Drop ASCAT files * apply changes from 2.5.1 to dev * bump version to 2.5.2dev * update CHANGELOG * update tiddit to 2.8.1 * Use Version 98 of Mouse * Add for grcm38 * Adjust mus musculus DB * Annotation * add smallerGRCh37 and minimalGRCh37 * use bwa aln when no knowIndels, otherwise use bwa mem, noIntervals currently in the process of being added everywhere * don't use bwa aln * add automatic generation of intervals file based on fastaFai file * Adjusted genomes.config * Should be list * Set genomes_base to something * Revert back * enable CreateIntervalsBed for intervals_list from GATK Bundle * Add proper calling list * Use the bed file * remove temp file * update CHANGELOG * Fix genome fa.fai * Add in mgpv5 * Try short track * Add in species handling * Document new parameter species * Add changelog * Fix iGenomes stuff * Add in note about GRCm38 * Fix small fai index issue * Adjusted quotes in genomes.config * And the same for igenomes * Better folder structure for Mouse Genome Project data * Minor adjustment to propoer paths * Apply suggestions from code review Add changes by Maxime Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com> * Remove space * Move it up * Update CHANGELOG.md Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com> * add minimal tests * fix processes with no intervals * add comments * params noIntervals -> no_intervals * sort genomes + add news * code polishing * update CHANGELOG * add split_fastq params to split the fastq files with the splitFastq() nf method * add tests * temporarely remove TIDDIT tests * add sention for bwa mem * disable docker and singularity * disable container * add fastaFai for bwamem * remove module samtools from label sentieon * fix output from bwa mem * fix output channel BamMapped from MapReads * set params.sentieon to null by default * add SentieonDedup process * fix typo * add fastaFai to SentieonDedup process * fix bam indexing * fix bam indexing * fix bam indexing * add SentieonBQSR * add label sentieon to SentieonBQSR * fix metrics output for SentieonBQSR * increase cpus for Sentieon BQSR * remove indexing * add index for dedup * bwa mem sentieon specific process * TSV file for sentieon Dedup * TSV for every step for Sentieon * recal -> deduped * fix input for TSV recalibrate * enable restart from recalibrate with TSV with Sentieon * fix sention variant calling from mapping and recalibrate * code polishing * add dump tag for imput sample * add dump tag for bamDedupedSentieon * code polishing * code polishing * code polishing * code polishing * remove when statement * fix typo * remove tsv for recalibrate with sentieon * add dnascope dnaseq * fix dnascope * add TNscope process * fix TNscope output * add pon for TNscope * add params.pon_index * add annotation for sention DNAseq, DNAscope, TNscope * add default pon_index * typo * fix typo * improve automatic annotation * typo * typo * add condition on when statement on TNscope * clean up * code polish * add CODEOWNERS file * add when statement on all sentieon processes with params.sentieon * remove munin sentieon specific configs from config * load sarek specific config * update path to specific config * update docs * remove Freebayes * update workflow image * remove old logo * fix tests * add docs about params split_fastq * update CHANGELOG * improve docs * more tests but less NF versions * actually run the tests * typo * simplify configs * add test for mpileup * go crazy with tests * fix tests * includ test.config * restore FreeBayes * remove label memory_max from BaseRecalibrator process to fix nf-core#72 * add --skipQC all and --tools Manta,mpileup,Strelka to minimal genome tests * update Nextflow version * update Nextflow version * update Nextflow * add --step annotation to profile * don't need to specify step here * move params initalization * add docs * fix markdownlint * more complete docs + sort genomes * improve tests * update docs * update CHANGELOG * improve script * fix tests * better comments * better comments * fix error on channel name * fix output for MergeBamRecal * fix MergeBamRecal output * fix TSV file * update comments and docs * add warning for sentieon only processes * nf-core bump-version . 2.5.2 * manual bump-version . 2.5.2 * update workflow image * downgrade tools for release * update CHANGELOG * clean up and update workflow image * allow a * fix workflow image * Apply suggestions from code review * Apply suggestions from code review * Update docs/output.md * Apply suggestions from code review * Apply suggestions from code review * Apply suggestions from code review * Reformats `bwa mem | samtools sort` command; WIP suboptimal resource usage * Addresses #5 ;WIP * Removes max_ resource alloc labels from MarkDuplicatesSpark * Replaces .md.bam.bai->.md.bai (same as nf-core) * Add ${markdup_java_options} to MarkDuplicatesSpark (same as nf-core MarkDuplicates) * Changes MarkDuplicates --verbosity, DEBUG->INFO * Changes intervalBed.simpleName->intervalBed.baseName; nf-cored * Removes label cpus_1 from BaseRecalibratorSpark * Remove cpus_2 labels from ApplyBQSRSpark; DEBUG->INFO * Changes pseudo file "no_vepFile.txt" from https to s3 link * Removes java options from ApplyBQSRSpark * Removes java options from MarkDupesSpark * Add java-options to MarkDupesSpark; verbosity INFO->ERROR * Fixes dupe --java-options; 🤦 * Attempt to fix MarkDupesSpark; "--lower-case"->"-CAP"; Removed tmp * Adds soft-coded allocation of resources to MapReads * Initialise params for MapReads split resource alloc * Adds neglected curlies around params * Adds neglected \ to bash vars * Adds neglected \ to bash vars * WIP; MapReads optimisations * Implement resource alloc between bwa and samtools * Adds max, med soft coded resource alloc * Re-labels processes (from hard coded resources to soft) * Adds extra curlies to addrees priority of eval * Add explicit declaration of maxForks/process * Update med resource allocation function * Add echo true and echo of ${bwa_cpus} and ${sort_cpus} * Hard code heap in MarkDuplicatesSpark at 8g * Correct expected output bai in MarkDupes * Removes Spark versions; Not stable with low resources * Removes sorting; Picard might sort? * Do not assume sorting in MarkDupes * Adds explicit --ASSUME_SORT_ORDER unsorted * Adds missing \\ * Omits -k 23 * Bringing sorted back * Eliminating pipes in mapping step * Adds bwa -k 23 and GenomeChronicler as tool (cgpu#16) - [x] Adds -k 23 (bwa mem seed length) - [x] Exposes as params bwa_cpus, sort_cpus - [x] Adds GenomeChronicler in tools (sarek logic) Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com> Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Szilveszter Juhos <szilveszter.juhos@scilifelab.se> Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com> Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Szilveszter Juhos <szilveszter.juhos@scilifelab.se>
cgpu
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Jan 21, 2020
* Absorbs latest nfcore and cgpu fork changes (#6) * nf-core bump-version . 2.5.1dev * Remove PublishDirMode from test profile (nf-core#40) * remove PublishDirMode from test profile * update all tools * minor updates + typo fix (nf-core#42) * minor updates + typo fix * fix VEP automated builds * add location for abstracts * remove reference to old buil.nf script * update CHANGELOG * Update docs/reference.md Co-Authored-By: Szilveszter Juhos <szilveszter.juhos@scilifelab.se> * Update docs/reference.md * Update docs/reference.md * Worfklow (nf-core#45) * Add workflow figure * Include workflow figure in readme * Update CHANGELOG * add minimal genome and update some processes * Start adding mouse data * Update iGenomes.config * Add tbi * Drop ASCAT files * apply changes from 2.5.1 to dev * bump version to 2.5.2dev * update CHANGELOG * update tiddit to 2.8.1 * Use Version 98 of Mouse * Add for grcm38 * Adjust mus musculus DB * Annotation * add smallerGRCh37 and minimalGRCh37 * use bwa aln when no knowIndels, otherwise use bwa mem, noIntervals currently in the process of being added everywhere * don't use bwa aln * add automatic generation of intervals file based on fastaFai file * Adjusted genomes.config * Should be list * Set genomes_base to something * Revert back * enable CreateIntervalsBed for intervals_list from GATK Bundle * Add proper calling list * Use the bed file * remove temp file * update CHANGELOG * Fix genome fa.fai * Add in mgpv5 * Try short track * Add in species handling * Document new parameter species * Add changelog * Fix iGenomes stuff * Add in note about GRCm38 * Fix small fai index issue * Adjusted quotes in genomes.config * And the same for igenomes * Better folder structure for Mouse Genome Project data * Minor adjustment to propoer paths * Apply suggestions from code review Add changes by Maxime Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com> * Remove space * Move it up * Update CHANGELOG.md Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com> * add minimal tests * fix processes with no intervals * add comments * params noIntervals -> no_intervals * sort genomes + add news * code polishing * update CHANGELOG * add split_fastq params to split the fastq files with the splitFastq() nf method * add tests * temporarely remove TIDDIT tests * add sention for bwa mem * disable docker and singularity * disable container * add fastaFai for bwamem * remove module samtools from label sentieon * fix output from bwa mem * fix output channel BamMapped from MapReads * set params.sentieon to null by default * add SentieonDedup process * fix typo * add fastaFai to SentieonDedup process * fix bam indexing * fix bam indexing * fix bam indexing * add SentieonBQSR * add label sentieon to SentieonBQSR * fix metrics output for SentieonBQSR * increase cpus for Sentieon BQSR * remove indexing * add index for dedup * bwa mem sentieon specific process * TSV file for sentieon Dedup * TSV for every step for Sentieon * recal -> deduped * fix input for TSV recalibrate * enable restart from recalibrate with TSV with Sentieon * fix sention variant calling from mapping and recalibrate * code polishing * add dump tag for imput sample * add dump tag for bamDedupedSentieon * code polishing * code polishing * code polishing * code polishing * remove when statement * fix typo * remove tsv for recalibrate with sentieon * add dnascope dnaseq * fix dnascope * add TNscope process * fix TNscope output * add pon for TNscope * add params.pon_index * add annotation for sention DNAseq, DNAscope, TNscope * add default pon_index * typo * fix typo * improve automatic annotation * typo * typo * add condition on when statement on TNscope * clean up * code polish * add CODEOWNERS file * add when statement on all sentieon processes with params.sentieon * remove munin sentieon specific configs from config * load sarek specific config * update path to specific config * update docs * remove Freebayes * update workflow image * remove old logo * fix tests * add docs about params split_fastq * update CHANGELOG * improve docs * more tests but less NF versions * actually run the tests * typo * simplify configs * add test for mpileup * go crazy with tests * fix tests * includ test.config * restore FreeBayes * remove label memory_max from BaseRecalibrator process to fix nf-core#72 * add --skipQC all and --tools Manta,mpileup,Strelka to minimal genome tests * update Nextflow version * update Nextflow version * update Nextflow * add --step annotation to profile * don't need to specify step here * move params initalization * add docs * fix markdownlint * more complete docs + sort genomes * improve tests * update docs * update CHANGELOG * improve script * fix tests * better comments * better comments * fix error on channel name * fix output for MergeBamRecal * fix MergeBamRecal output * fix TSV file * update comments and docs * add warning for sentieon only processes * nf-core bump-version . 2.5.2 * manual bump-version . 2.5.2 * update workflow image * downgrade tools for release * update CHANGELOG * clean up and update workflow image * allow a * fix workflow image * Apply suggestions from code review * Apply suggestions from code review * Update docs/output.md * Apply suggestions from code review * Apply suggestions from code review * Apply suggestions from code review * Reformats `bwa mem | samtools sort` command; WIP suboptimal resource usage * Addresses #5 ;WIP * Removes max_ resource alloc labels from MarkDuplicatesSpark * Replaces .md.bam.bai->.md.bai (same as nf-core) * Add ${markdup_java_options} to MarkDuplicatesSpark (same as nf-core MarkDuplicates) * Changes MarkDuplicates --verbosity, DEBUG->INFO * Changes intervalBed.simpleName->intervalBed.baseName; nf-cored * Removes label cpus_1 from BaseRecalibratorSpark * Remove cpus_2 labels from ApplyBQSRSpark; DEBUG->INFO * Changes pseudo file "no_vepFile.txt" from https to s3 link * Removes java options from ApplyBQSRSpark * Removes java options from MarkDupesSpark * Add java-options to MarkDupesSpark; verbosity INFO->ERROR * Fixes dupe --java-options; 🤦 * Attempt to fix MarkDupesSpark; "--lower-case"->"-CAP"; Removed tmp * Adds soft-coded allocation of resources to MapReads * Initialise params for MapReads split resource alloc * Adds neglected curlies around params * Adds neglected \ to bash vars * Adds neglected \ to bash vars * WIP; MapReads optimisations * Implement resource alloc between bwa and samtools * Adds max, med soft coded resource alloc * Re-labels processes (from hard coded resources to soft) * Adds extra curlies to addrees priority of eval * Add explicit declaration of maxForks/process * Update med resource allocation function * Add echo true and echo of ${bwa_cpus} and ${sort_cpus} * Hard code heap in MarkDuplicatesSpark at 8g * Correct expected output bai in MarkDupes * Removes Spark versions; Not stable with low resources * Removes sorting; Picard might sort? * Do not assume sorting in MarkDupes * Adds explicit --ASSUME_SORT_ORDER unsorted * Adds missing \\ * Omits -k 23 * Bringing sorted back * Eliminating pipes in mapping step * Adds bwa -k 23 and GenomeChronicler as tool (cgpu#16) - [x] Adds -k 23 (bwa mem seed length) - [x] Exposes as params bwa_cpus, sort_cpus - [x] Adds GenomeChronicler in tools (sarek logic) Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com> Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Szilveszter Juhos <szilveszter.juhos@scilifelab.se> * Replaces intervals process to be flexible * Updated nextflow.config with new intervals process * Updates conf/base.config; Removes dynamic resource alloc Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com> Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Szilveszter Juhos <szilveszter.juhos@scilifelab.se>
cgpu
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Jan 22, 2020
* nf-core bump-version . 2.5.1dev * Remove PublishDirMode from test profile (nf-core#40) * remove PublishDirMode from test profile * update all tools * minor updates + typo fix (nf-core#42) * minor updates + typo fix * fix VEP automated builds * add location for abstracts * remove reference to old buil.nf script * update CHANGELOG * Update docs/reference.md Co-Authored-By: Szilveszter Juhos <szilveszter.juhos@scilifelab.se> * Update docs/reference.md * Update docs/reference.md * Worfklow (nf-core#45) * Add workflow figure * Include workflow figure in readme * Update CHANGELOG * add minimal genome and update some processes * Start adding mouse data * Update iGenomes.config * Add tbi * Drop ASCAT files * apply changes from 2.5.1 to dev * bump version to 2.5.2dev * update CHANGELOG * update tiddit to 2.8.1 * Use Version 98 of Mouse * Add for grcm38 * Adjust mus musculus DB * Annotation * add smallerGRCh37 and minimalGRCh37 * use bwa aln when no knowIndels, otherwise use bwa mem, noIntervals currently in the process of being added everywhere * don't use bwa aln * add automatic generation of intervals file based on fastaFai file * Adjusted genomes.config * Should be list * Set genomes_base to something * Revert back * enable CreateIntervalsBed for intervals_list from GATK Bundle * Add proper calling list * Use the bed file * remove temp file * update CHANGELOG * Fix genome fa.fai * Add in mgpv5 * Try short track * Add in species handling * Document new parameter species * Add changelog * Fix iGenomes stuff * Add in note about GRCm38 * Fix small fai index issue * Adjusted quotes in genomes.config * And the same for igenomes * Better folder structure for Mouse Genome Project data * Minor adjustment to propoer paths * Apply suggestions from code review Add changes by Maxime Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com> * Remove space * Move it up * Update CHANGELOG.md Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com> * add minimal tests * fix processes with no intervals * add comments * params noIntervals -> no_intervals * sort genomes + add news * code polishing * update CHANGELOG * add split_fastq params to split the fastq files with the splitFastq() nf method * add tests * temporarely remove TIDDIT tests * add sention for bwa mem * disable docker and singularity * disable container * add fastaFai for bwamem * remove module samtools from label sentieon * fix output from bwa mem * fix output channel BamMapped from MapReads * set params.sentieon to null by default * add SentieonDedup process * fix typo * add fastaFai to SentieonDedup process * fix bam indexing * fix bam indexing * fix bam indexing * add SentieonBQSR * add label sentieon to SentieonBQSR * fix metrics output for SentieonBQSR * increase cpus for Sentieon BQSR * remove indexing * add index for dedup * bwa mem sentieon specific process * TSV file for sentieon Dedup * TSV for every step for Sentieon * recal -> deduped * fix input for TSV recalibrate * enable restart from recalibrate with TSV with Sentieon * fix sention variant calling from mapping and recalibrate * code polishing * add dump tag for imput sample * add dump tag for bamDedupedSentieon * code polishing * code polishing * code polishing * code polishing * remove when statement * fix typo * remove tsv for recalibrate with sentieon * add dnascope dnaseq * fix dnascope * add TNscope process * fix TNscope output * add pon for TNscope * add params.pon_index * add annotation for sention DNAseq, DNAscope, TNscope * add default pon_index * typo * fix typo * improve automatic annotation * typo * typo * add condition on when statement on TNscope * clean up * code polish * add CODEOWNERS file * add when statement on all sentieon processes with params.sentieon * remove munin sentieon specific configs from config * load sarek specific config * update path to specific config * update docs * remove Freebayes * update workflow image * remove old logo * fix tests * add docs about params split_fastq * update CHANGELOG * improve docs * more tests but less NF versions * actually run the tests * typo * simplify configs * add test for mpileup * go crazy with tests * fix tests * includ test.config * restore FreeBayes * remove label memory_max from BaseRecalibrator process to fix nf-core#72 * add --skipQC all and --tools Manta,mpileup,Strelka to minimal genome tests * update Nextflow version * update Nextflow version * update Nextflow * add --step annotation to profile * don't need to specify step here * move params initalization * add docs * fix markdownlint * more complete docs + sort genomes * improve tests * update docs * update CHANGELOG * improve script * fix tests * better comments * better comments * fix error on channel name * fix output for MergeBamRecal * fix MergeBamRecal output * fix TSV file * update comments and docs * add warning for sentieon only processes * nf-core bump-version . 2.5.2 * manual bump-version . 2.5.2 * update workflow image * downgrade tools for release * update CHANGELOG * clean up and update workflow image * allow a * fix workflow image * Apply suggestions from code review * Apply suggestions from code review * Update docs/output.md * Apply suggestions from code review * Apply suggestions from code review * Apply suggestions from code review * Reformats `bwa mem | samtools sort` command; WIP suboptimal resource usage * Addresses #5 ;WIP * Removes max_ resource alloc labels from MarkDuplicatesSpark * Replaces .md.bam.bai->.md.bai (same as nf-core) * Add ${markdup_java_options} to MarkDuplicatesSpark (same as nf-core MarkDuplicates) * Changes MarkDuplicates --verbosity, DEBUG->INFO * Changes intervalBed.simpleName->intervalBed.baseName; nf-cored * Removes label cpus_1 from BaseRecalibratorSpark * Remove cpus_2 labels from ApplyBQSRSpark; DEBUG->INFO * Changes pseudo file "no_vepFile.txt" from https to s3 link * Removes java options from ApplyBQSRSpark * Removes java options from MarkDupesSpark * Add java-options to MarkDupesSpark; verbosity INFO->ERROR * Fixes dupe --java-options; 🤦 * Attempt to fix MarkDupesSpark; "--lower-case"->"-CAP"; Removed tmp * Adds soft-coded allocation of resources to MapReads * Initialise params for MapReads split resource alloc * Adds neglected curlies around params * Adds neglected \ to bash vars * Adds neglected \ to bash vars * WIP; MapReads optimisations * Implement resource alloc between bwa and samtools * Adds max, med soft coded resource alloc * Re-labels processes (from hard coded resources to soft) * Adds extra curlies to addrees priority of eval * Add explicit declaration of maxForks/process * Update med resource allocation function * Add echo true and echo of ${bwa_cpus} and ${sort_cpus} * Hard code heap in MarkDuplicatesSpark at 8g * Correct expected output bai in MarkDupes * Removes Spark versions; Not stable with low resources * Removes sorting; Picard might sort? * Do not assume sorting in MarkDupes * Adds explicit --ASSUME_SORT_ORDER unsorted * Adds missing \\ * Omits -k 23 * Bringing sorted back * Eliminating pipes in mapping step * Adds bwa -k 23 and GenomeChronicler as tool (cgpu#16) - [x] Adds -k 23 (bwa mem seed length) - [x] Exposes as params bwa_cpus, sort_cpus - [x] Adds GenomeChronicler in tools (sarek logic) Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com> Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Szilveszter Juhos <szilveszter.juhos@scilifelab.se>
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