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Releases: TheJacksonLaboratory/cs-nf-pipelines

v0.3.0

18 May 15:42
@MikeWLloyd MikeWLloyd
v0.3.0
55f3c23
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v0.3.0

Release v0.3.0

In this major release we have added two additional pipelines, added flexibility for specifying inputs via sample sheets, support for downloading remote input data, support for GRCm39, support for PDX data, and many more changes detailed below. Additionally, we have added the concept of "subworkflows" for tasks that are more complex than a module and/or involve multiple containers, yet can be potentially re-used in multiple pipelines.

Pipelines Added:

  1. ChIP-seq - human, mouse
  2. Paired Tumor Analysis (somatic/germline WGS) - human, PDX
  3. RNA Fusion - human, PDX

Subworkflows Added:

  1. Aria download for remote input data
  2. Concatenate paired tumor/normal FASTQ files
  3. RNA-seq for PDX input data

Modules Added:

  1. arriba/arriba.nf
  2. bamtools/bamtools_filter.nf
  3. bcftools/bcftools_germline_filter.nf
  4. bcftools/bcftools_intersect_lancet_candidates.nf
  5. bcftools/bcftools_merge_callers.nf
  6. bcftools/bcftools_remove_spanning.nf
  7. bcftools/bcftools_split_multiallelic_regions.nf
  8. bcftools/bcftools_split_multiallelic.nf
  9. bedtools/bedtools_amplicon_metrics.nf
  10. bedtools/bedtools_genomecov.nf
  11. bedtools/bedtools_start_candidates.nf
  12. biqseq2/bicseq2_normalize.nf
  13. biqseq2/bicseq2_seg_unpaired.nf
  14. biqseq2/bicseq2_seg.nf
  15. conpair/conpair_pileup.nf
  16. conpair/conpair.nf
  17. cosmic/cosmic_add_cancer_resistance_mutations_germline.nf
  18. cosmic/cosmic_add_cancer_resistance_mutations_somatic.nf
  19. cosmic/cosmic_annotation_somatic.nf
  20. cosmic/cosmic_annotation.nf
  21. deeptools/deeptools_computematrix.nf
  22. deeptools/deeptools_plotfingerprint.nf
  23. deeptools/deeptools_plotheatmap.nf
  24. deeptools/deeptools_plotprofile.nf
  25. ensembl/varianteffectpredictor_germline.nf
  26. ensembl/varianteffectpredictor_somatic.nf
  27. fastq-tools/fastq-pair.nf
  28. fastq-tools/fastq-sort.nf
  29. fusion_report/fusion_report.nf
  30. fusioncatcher/fusioncatcher.nf
  31. gatk/gatk_cnnscorevariants.nf
  32. gatk/gatk_combinegvcfs.nf
  33. gatk/gatk_filtermutectcalls_tumorOnly.nf
  34. gatk/gatk_filtermutectcalls.nf
  35. gatk/gatk_filtervarianttranches.nf
  36. gatk/gatk_genotype_gvcf.nf
  37. gatk/gatk_getsamplename_noMeta.nf
  38. gatk/gatk_getsamplename.nf
  39. gatk/gatk_haplotypecaller_sv_germline.nf
  40. gatk/gatk_mergemutectstats.nf
  41. gatk/gatk_mutect2_tumorOnly.nf
  42. gatk/gatk_mutect2.nf
  43. gatk/gatk_sortvcf_germline.nf
  44. gatk/gatk_sortvcf_somatic_merge.nf
  45. gatk/gatk_sortvcf_somatic_tools.nf
  46. gatk/gatk_variantfiltration_af.nf
  47. gatk/gatk_variantfiltration_mutect2.nf
  48. gatk/gatk3_applyrecalibration.nf
  49. gatk/gatk3_genotypegvcf.nf
  50. gatk/gatk3_haplotypecaller.nf
  51. gatk/gatk3_indelrealigner.nf
  52. gatk/gatk3_realignertargetcreator.nf
  53. gatk/gatk3_variantannotator.nf
  54. gatk/gatk3_variantrecalibrator.nf
  55. gridss/gridss_assemble.nf
  56. gridss/gridss_calling.nf
  57. gridss/gridss_chrom_filter.nf
  58. gridss/gridss_preprocess.nf
  59. gridss/gripss_somatic_filter.nf
  60. homer/annotate_boolean_peaks.nf
  61. homer/homer_annotatepeaks.nf
  62. homer/plot_homer_annotatepeaks.nf
  63. illumina/manta.nf
  64. illumina/strelka2.nf
  65. jaffa/jaffa.nf
  66. kallisto/kallisto_insert_size.nf
  67. kallisto/kallisto_quant.nf
  68. lumpy_sv/lumpy_sv.nf
  69. macs2/macs2_consensus.nf
  70. macs2/macs2_peak_calling_chipseq.nf
  71. macs2/plot_macs2_qc.nf
  72. msisensor2/msisensor2_tumorOnly.nf
  73. msisensor2/msisensor2.nf
  74. multiqc/multiqc_custom_phantompeakqualtools.nf
  75. novocraft/novosort.nf
  76. nygc-short-alignment-marking/short_alignment_marking.nf
  77. nygenome/lancet_confirm.nf
  78. nygenome/lancet.nf
  79. phantompeakqualtools/phantompeakqualtools.nf
  80. picard/picard_cleansam.nf
  81. picard/picard_collectmultiplemetrics.nf
  82. picard/picard_collecttargetpcrmetrics.nf
  83. picard/picard_fix_mate_information.nf
  84. picard/picard_mergesamfiles.nf
  85. pizzly/pizzly.nf
  86. preseq/preseq.nf
  87. primerclip/primerclip.nf
  88. python/python_add_final_allele_counts.nf
  89. python/python_add_nygc_allele_counts.nf
  90. python/python_check_strandedness.nf
  91. python/python_filter_pon.nf
  92. python/python_filter_vcf.nf
  93. python/python_germline_vcf_finalization.nf
  94. python/python_get_candidates.nf
  95. python/python_merge_columns.nf
  96. python/python_merge_prep.nf
  97. python/python_remove_contig.nf
  98. python/python_rename_metadata.nf
  99. python/python_rename_vcf.nf
  100. python/python_reorder_vcf_columns.nf
  101. python/python_snv_to_mnv_final_filter.nf
  102. python/python_somatic_vcf_finalization.nf
  103. python/python_split_mnv.nf
  104. python/python_vcf_to_bed.nf
  105. r/annotate_bicseq2_cnv.nf
  106. r/annotate_genes_sv.nf
  107. r/annotate_sv_with_cnv.nf
  108. r/annotate_sv.nf
  109. r/filter_bedpe.nf
  110. r/frag_len_plot.nf
  111. r/merge_sv.nf
  112. samtools/samtools_faidx.nf
  113. samtools/samtools_filter_unique_reads.nf
  114. samtools/samtools_filter.nf
  115. samtools/samtools_mergebam_filter.nf
  116. samtools/samtools_stats_insertsize.nf
  117. samtools/samtools_stats.nf
  118. samtools/samtools_view.nf
  119. squid/squid_annotate.nf
  120. squid/squid_call.nf
  121. star/star_align.nf
  122. star-fusion/star-fusion.nf
  123. subread/subread_feature_counts_chipseq.nf
  124. svaba/svaba.nf
  125. tabix/compress_merged_vcf.nf
  126. tabix/compress_vcf_region.nf
  127. tabix/compress_vcf.nf
  128. ucsc/ucsc_bedgraphtobigwig.nf
  129. utility_modules/aria_download.nf
  130. utility_modules/chipseq_bampe_rm_orphan.nf
  131. utility_modules/chipseq_check_design.nf
  132. utility_modules/chipseq_make_genome_filter.nf
  133. utility_modules/concatenate_reads_sampleSheet.nf
  134. utility_modules/deseq2_qc.nf
  135. utility_modules/frip_score.nf
  136. utility_modules/get_read_length.nf
  137. utility_modules/gunzip.nf
  138. utility_modules/jax_trimmer.nf
  139. utility_modules/parse_extracted_sv_table.nf
  140. xenome/xenome.nf

Pipeline Changes:

  1. WES, RNA-seq, and RNA-fusion added support for PDX data
  2. WES, RNA-seq, WGS, ATAC, RRBS, ChIP added support for GRCm39
  3. Support for input specification using sample sheets for ATAC, RNA-seq, RRBS, WES, WGS
  4. Support for downloading input data for ATAC, RNA-seq, RRBS, WES, WGS
  5. Added MULTIQC to ATAC, RNA-seq, RRBS, WES, WGS
  6. Added assessment of strandedness using python/python_check_strandedness.nf rather than requiring specification via parameters
  7. Added assessment of read length for RNAseq for STAR index selection rather than requiring specfication via parameters
  8. Modified variant annotations in WES and WGS
  9. Added GVCF support for WES and WGS

Module Changes:

  1. errorStrategy modified for all modules to catch and report instances where tasks fail due to walltime or memory contraints. This previously required a deep reading of the subtask SLURM logs, but now will be reported in the top-level SLURM log and is more user-friendly
  2. Removed log.info statements from modules to avoid noisy disruption of log files
  3. ChIP-seq support for bwa/bwa_mem.nf, fastqc/fastqc.nf, picard/picard_markduplicates.nf, trim_galore/trim_galore.nf
  4. Corrected emit statements for g2gtools/g2gtools_chain_convert_peak.nf
  5. Corrected emit statements for gatk/gatk_chain_filter_reads.nf
  6. Modified gatk/gatk_haplotypecaller_interval.nf and gatk/gatk_haplotypecaller.nf for optional GVCF support
  7. Generalized multiqc/multiqc.nf via parameter for multiqc config
  8. Removed --METRIC_ACCUMULATION_LEVEL ALL_READS and --VALIDATION_STRINGENCY LENIENT parameters from picard/picard_collectalignmentsummarymetrics.nf
  9. Modified strand specification logic for picard/picard_collectrnaseqmetrics.nf
  10. Updated rsem/rsem_alignment_expression.nf to reflect changes in strandedness detection, reorganized outputs and catching log files for multiqc
  11. Changes to output text for mt DNA content in samtools/samtools_calc_mtdna_filter_chrm.nf
  12. Changes to output text from samtools/samtools_final_calc_frip.nf
  13. Changes to output formatting for samtools/samtools_quality_checks.nf
  14. Updated snpEff container to v5.1d to support GRCm39
  15. Changes to output fields for mouse and human from snpeff_snpsift/snpsift_extractfields.nf
  16. Added missing container to utility_modules/concatenate_reads_PE.nf and utility_modules/concatenate_reads_SE.nf
Assets 2
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v0.2.2

07 Mar 16:59
@MikeWLloyd MikeWLloyd
v0.2.2
4794b91
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v0.2.2

Release 0.2.2

  • Change WES and WGS COMSIC annotation to use SNPsift.
  • Added explicit dbSNP annotation.

Pipelines Added:

NONE

Modules Added:

  1. SNPSIFT_ANNOTATE

Pipeline Changes:

  1. WES and WGS now use SNPSift to annotate COSMIC and dbSNP IDs onto variants.

Module Changes:

  1. COSMIC_ANNOTATION and associated perl scripts removed.
Assets 2
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v0.2.1

01 Feb 21:12
@BrianSanderson BrianSanderson
v0.2.1
bf8d0a8
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v0.2.1

RELEASE NOTES

Release 0.2.1

Added STAR support to RNA-seq pipeline.

Pipelines Added:

NONE

Modules Added:

NONE

Pipeline Changes:

  1. RNA-seq pipeline now supports STAR and bowtie2 (default) through the RSEM module.

Module Changes:

  1. RSEM: --rsem_aligner accepts "bowtie2" or "star." The default STAR indices for mouse and human are 100 bp, with alternates suggested in the RNA-seq config file.

Release 0.2.0

NOTE: This release contains a patch for multi-sample processing. We strongly recommend multi-sample processing done prior to this release should be re-run with v0.2.0+

Pipelines Added:

  1. RRBS - Mouse & Human
  2. ATAC - Mouse & Human

Modules Added:

  1. FastQC
  2. Trim-Galore
  3. Bismark Alignment
  4. Bismark Deduplicator
  5. Bismark Methylation Extractor
  6. MultiQC
  7. Bedtools functions for ATAC QC summary
  8. Bowtie2
  9. Cutadapt
  10. Deeptools bamcoverage and alignmentSieve
  11. g2gTools chain convert
  12. Macs2 ATAC peak calling and ATAC peak coverage
  13. Subread feature counts

Pipeline Changes:

  1. Multiple pipeline changes related to multi-sample patch.
  2. Modified module load statements to invoke "${projectDir}" instead of relative "../" path.
  3. Removed CTP and Probe coverage calculations from human RNA-seq

Module Changes:

  1. Multiple module changes related to multi-sample patch.
  2. Trimmomatic Trim stub module removed.
  3. RSEM - forward stranded option added.
  4. Picard Collect RNAseqMetrics - forward strand option added.

Release 0.1.2

Updated run scripts to load CS supported Nextflow module.

Release 0.1.1

Pipelines Added:

NONE

Modules Added:

  1. concatenate_reads_PE.nf
  2. concatenate_reads_SE.nf
  3. Modules refactored to individual files (e.g., gatk_haplotypecaller.nf).

Pipeline Changes:

  1. Added ability to concatenate Fastq files by sample, which are split across sequencing lanes into single R1/R2 or R1 files (depending on PE or SE).
  2. Adjusted pipelines for refactored module files.
  3. Fixed CTP/PROBE typo in human RNA coverage calculation.
  4. Added HPC --profile options and settings for Sumner and Elion.

Module Changes:

  1. Adjusted WGS wall clock settings.
  2. Refactored modules to individual files (e.g., gatk_haplotypecaller.nf).
  3. Set pipeline script parameter to hard coded paths.
  4. Cleaned all Nextflow files from the bin directory.
  5. Removed Sumner specific HPC settings from each module.

Release 0.1.0 -- 03.28.2022

Pipelines Added:

  1. Whole Genome Sequencing - Mouse & Human
  2. Whole Exome Sequencing - Mouse & Human
  3. RNA Sequencing - Mouse & Human

Modules Added:

  1. bamtools.nf
  2. bcftools.nf
  3. bwa.nf
  4. cosmic.nf
  5. gatk.nf
  6. picard.nf
  7. quality_stats.nf
  8. read_groups.nf
  9. rsem.nf
  10. samtools.nf
  11. snpeff.nf
  12. snpsift.nf
  13. summary_stats.nf
  14. trimmomatic.nf

Pipeline Changes:

NONE

Module Changes:

NONE

Assets 2
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v0.2.0

24 Oct 18:27
@MikeWLloyd MikeWLloyd
v0.2.0
6fc6a1d
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v0.2.0

RELEASE NOTES

Release 0.2.0

NOTE: This release contains a patch for multi-sample processing. We strongly recommend multi-sample processing done prior to this release should be re-run with v0.2.0+

Pipelines Added:

  1. RRBS - Mouse & Human
  2. ATAC - Mouse & Human

Modules Added:

  1. FastQC
  2. Trim-Galore
  3. Bismark Alignment
  4. Bismark Deduplicator
  5. Bismark Methylation Extractor
  6. MultiQC
  7. Bedtools functions for ATAC QC summary
  8. Bowtie2
  9. Cutadapt
  10. Deeptools bamcoverage and alignmentSieve
  11. g2gTools chain convert
  12. Macs2 ATAC peak calling and ATAC peak coverage
  13. Subread feature counts

Pipeline Changes:

  1. Multiple pipeline changes related to multi-sample patch.
  2. Modified module load statements to invoke "${projectDir}" instead of relative "../" path.
  3. Removed CTP and Probe coverage calculations from human RNA-seq

Module Changes:

  1. Multiple module changes related to multi-sample patch.
  2. Trimmomatic Trim stub module removed.
  3. RSEM - forward stranded option added.
  4. Picard Collect RNAseqMetrics - forward strand option added.

Release 0.1.2

Updated run scripts to load CS supported Nextflow module.

Release 0.1.1

Pipelines Added:

NONE

Modules Added:

  1. concatenate_reads_PE.nf
  2. concatenate_reads_SE.nf
  3. Modules refactored to individual files (e.g., gatk_haplotypecaller.nf).

Pipeline Changes:

  1. Added ability to concatenate Fastq files by sample, which are split across sequencing lanes into single R1/R2 or R1 files (depending on PE or SE).
  2. Adjusted pipelines for refactored module files.
  3. Fixed CTP/PROBE typo in human RNA coverage calculation.
  4. Added HPC --profile options and settings for Sumner and Elion.

Module Changes:

  1. Adjusted WGS wall clock settings.
  2. Refactored modules to individual files (e.g., gatk_haplotypecaller.nf).
  3. Set pipeline script parameter to hard coded paths.
  4. Cleaned all Nextflow files from the bin directory.
  5. Removed Sumner specific HPC settings from each module.

Release 0.1.0 -- 03.28.2022

Pipelines Added:

  1. Whole Genome Sequencing - Mouse & Human
  2. Whole Exome Sequencing - Mouse & Human
  3. RNA Sequencing - Mouse & Human

Modules Added:

  1. bamtools.nf
  2. bcftools.nf
  3. bwa.nf
  4. cosmic.nf
  5. gatk.nf
  6. picard.nf
  7. quality_stats.nf
  8. read_groups.nf
  9. rsem.nf
  10. samtools.nf
  11. snpeff.nf
  12. snpsift.nf
  13. summary_stats.nf
  14. trimmomatic.nf

Pipeline Changes:

NONE

Module Changes:

NONE

Assets 2
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