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Update spring/decompress-module #1573

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merged 10 commits into from
Jul 8, 2024
Merged

Update spring/decompress-module #1573

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7a63a85
Improved config of spring/decompress
asp8200 Jun 19, 2024
f963873
Added extension .spring to file-extension for spring-files
asp8200 Jun 19, 2024
6082147
patch for spring/decompress
asp8200 Jun 19, 2024
7f3b4b6
Replace ext.one_direction with meta.one_strand
asp8200 Jun 20, 2024
6c15d6b
update patch of spring/decompress
asp8200 Jun 20, 2024
e6b2e5c
Changing SPRING_DECOMPRESS_TO_R1_FQ_PAIR to SPRING_DECOMPRESS_TO_R1_F…
asp8200 Jun 20, 2024
77a9a0f
Updating module for spring/decompress
asp8200 Jun 24, 2024
b2503f0
Update changelog
asp8200 Jun 24, 2024
e749a7e
Fixing indentation
asp8200 Jun 24, 2024
455b0a2
remove patch line
FriederikeHanssen Jul 1, 2024
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -10,7 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added

- [#1502](https://github.com/nf-core/sarek/pull/1502) - export CNVs into VCF format in `bam_variant_calling_cnvkit`
- [#1534](https://github.com/nf-core/sarek/pull/1534) - Handling `.fastq.gz.spring` files as input
- [#1534](https://github.com/nf-core/sarek/pull/1534), [#1573](https://github.com/nf-core/sarek/pull/1573) - Handling `.fastq.gz.spring` files as input

### Changed

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4 changes: 2 additions & 2 deletions docs/usage.md
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Expand Up @@ -89,8 +89,8 @@ Output from Variant Calling and/or Annotation will be in a specific directory fo
| `lane` | Lane ID, used when the `sample` is multiplexed on several lanes. Must be unique for each lane in the same sample (but does not need to be the original lane name), and must contain at least one character <br /> _Required for `--step mapping`_ |
| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension `.fastq.gz` or `.fq.gz`. |
| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension `.fastq.gz` or `.fq.gz`. |
| `spring_1` | Full path to spring-compressed, gzipped FastQ file for read 1 or for reads 1 and 2. The Fastq file has to be first gzipped, then spring-compressed, and it must have the extension `.fastq.gz` or `.fq.gz`. |
| `spring_2` | Full path to spring-compressed, gzipped FastQ file for read 2. The Fastq file has to be first gzipped, then spring-compressed, and it must have the extension `.fastq.gz` or `.fq.gz`. |
| `spring_1` | Full path to spring-compressed, gzipped FastQ file for read 1 or for reads 1 and 2. The Fastq file has to be first gzipped, then spring-compressed, and it must have the extension `.fastq.gz.spring` or `.fq.gz.spring`. |
| `spring_2` | Full path to spring-compressed, gzipped FastQ file for read 2. The Fastq file has to be first gzipped, then spring-compressed, and it must have the extension `.fastq.gz.spring` or `.fq.gz.spring`. |
| `bam` | Full path to (u)BAM file |
| `bai` | Full path to BAM index file |
| `cram` | Full path to CRAM file |
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -451,7 +451,7 @@
},
"spring/decompress": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"git_sha": "0a92fa8d17d9e3c411e01a0ce41a86eff02b1599",
"installed_by": ["modules"]
},
"strelka/germline": {
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3 changes: 2 additions & 1 deletion modules/nf-core/spring/decompress/main.nf
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7 changes: 6 additions & 1 deletion modules/nf-core/spring/decompress/meta.yml
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90 changes: 48 additions & 42 deletions workflows/sarek/main.nf
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Expand Up @@ -4,87 +4,87 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { paramsSummaryMap } from 'plugin/nf-validation'
include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_sarek_pipeline'
include { paramsSummaryMap } from 'plugin/nf-validation'
include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_sarek_pipeline'

// Create samplesheets to restart from different steps
include { CHANNEL_ALIGN_CREATE_CSV } from '../../subworkflows/local/channel_align_create_csv/main'
include { CHANNEL_MARKDUPLICATES_CREATE_CSV } from '../../subworkflows/local/channel_markduplicates_create_csv/main'
include { CHANNEL_BASERECALIBRATOR_CREATE_CSV } from '../../subworkflows/local/channel_baserecalibrator_create_csv/main'
include { CHANNEL_APPLYBQSR_CREATE_CSV } from '../../subworkflows/local/channel_applybqsr_create_csv/main'
include { CHANNEL_VARIANT_CALLING_CREATE_CSV } from '../../subworkflows/local/channel_variant_calling_create_csv/main'
include { CHANNEL_ALIGN_CREATE_CSV } from '../../subworkflows/local/channel_align_create_csv/main'
include { CHANNEL_MARKDUPLICATES_CREATE_CSV } from '../../subworkflows/local/channel_markduplicates_create_csv/main'
include { CHANNEL_BASERECALIBRATOR_CREATE_CSV } from '../../subworkflows/local/channel_baserecalibrator_create_csv/main'
include { CHANNEL_APPLYBQSR_CREATE_CSV } from '../../subworkflows/local/channel_applybqsr_create_csv/main'
include { CHANNEL_VARIANT_CALLING_CREATE_CSV } from '../../subworkflows/local/channel_variant_calling_create_csv/main'

// Convert BAM files to FASTQ files
include { BAM_CONVERT_SAMTOOLS as CONVERT_FASTQ_INPUT } from '../../subworkflows/local/bam_convert_samtools/main'
include { BAM_CONVERT_SAMTOOLS as CONVERT_FASTQ_UMI } from '../../subworkflows/local/bam_convert_samtools/main'
include { BAM_CONVERT_SAMTOOLS as CONVERT_FASTQ_INPUT } from '../../subworkflows/local/bam_convert_samtools/main'
include { BAM_CONVERT_SAMTOOLS as CONVERT_FASTQ_UMI } from '../../subworkflows/local/bam_convert_samtools/main'

// Convert fastq.gz.spring files to fastq.gz files
include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_R1_FQ_PAIR } from '../../modules/nf-core/spring/decompress/main'
include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_R2_FQ_PAIR } from '../../modules/nf-core/spring/decompress/main'
include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_FQ_PAIR } from '../../modules/nf-core/spring/decompress/main'
include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_R1_FQ } from '../../modules/nf-core/spring/decompress/main'
include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_R2_FQ } from '../../modules/nf-core/spring/decompress/main'
include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_FQ_PAIR } from '../../modules/nf-core/spring/decompress/main'

// Run FASTQC
include { FASTQC } from '../../modules/nf-core/fastqc/main'
include { FASTQC } from '../../modules/nf-core/fastqc/main'

// TRIM/SPLIT FASTQ Files
include { FASTP } from '../../modules/nf-core/fastp/main'
include { FASTP } from '../../modules/nf-core/fastp/main'

// Create umi consensus bams from fastq
include { FASTQ_CREATE_UMI_CONSENSUS_FGBIO } from '../../subworkflows/local/fastq_create_umi_consensus_fgbio/main'
include { FASTQ_CREATE_UMI_CONSENSUS_FGBIO } from '../../subworkflows/local/fastq_create_umi_consensus_fgbio/main'

// Map input reads to reference genome
include { FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON } from '../../subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main'
include { FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON } from '../../subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main'

// Merge and index BAM files (optional)
include { BAM_MERGE_INDEX_SAMTOOLS } from '../../subworkflows/local/bam_merge_index_samtools/main'
include { BAM_MERGE_INDEX_SAMTOOLS } from '../../subworkflows/local/bam_merge_index_samtools/main'

// Convert BAM files
include { SAMTOOLS_CONVERT as BAM_TO_CRAM } from '../../modules/nf-core/samtools/convert/main'
include { SAMTOOLS_CONVERT as BAM_TO_CRAM_MAPPING } from '../../modules/nf-core/samtools/convert/main'
include { SAMTOOLS_CONVERT as BAM_TO_CRAM } from '../../modules/nf-core/samtools/convert/main'
include { SAMTOOLS_CONVERT as BAM_TO_CRAM_MAPPING } from '../../modules/nf-core/samtools/convert/main'

// Convert CRAM files (optional)
include { SAMTOOLS_CONVERT as CRAM_TO_BAM } from '../../modules/nf-core/samtools/convert/main'
include { SAMTOOLS_CONVERT as CRAM_TO_BAM_RECAL } from '../../modules/nf-core/samtools/convert/main'
include { SAMTOOLS_CONVERT as CRAM_TO_BAM } from '../../modules/nf-core/samtools/convert/main'
include { SAMTOOLS_CONVERT as CRAM_TO_BAM_RECAL } from '../../modules/nf-core/samtools/convert/main'

// Mark Duplicates (+QC)
include { BAM_MARKDUPLICATES } from '../../subworkflows/local/bam_markduplicates/main'
include { BAM_MARKDUPLICATES_SPARK } from '../../subworkflows/local/bam_markduplicates_spark/main'
include { BAM_SENTIEON_DEDUP } from '../../subworkflows/local/bam_sentieon_dedup/main'
include { BAM_MARKDUPLICATES } from '../../subworkflows/local/bam_markduplicates/main'
include { BAM_MARKDUPLICATES_SPARK } from '../../subworkflows/local/bam_markduplicates_spark/main'
include { BAM_SENTIEON_DEDUP } from '../../subworkflows/local/bam_sentieon_dedup/main'

// QC on CRAM
include { CRAM_QC_MOSDEPTH_SAMTOOLS as CRAM_QC_NO_MD } from '../../subworkflows/local/cram_qc_mosdepth_samtools/main'
include { CRAM_SAMPLEQC } from '../../subworkflows/local/cram_sampleqc/main'
include { CRAM_QC_MOSDEPTH_SAMTOOLS as CRAM_QC_NO_MD } from '../../subworkflows/local/cram_qc_mosdepth_samtools/main'
include { CRAM_SAMPLEQC } from '../../subworkflows/local/cram_sampleqc/main'

// Create recalibration tables
include { BAM_BASERECALIBRATOR } from '../../subworkflows/local/bam_baserecalibrator/main'
include { BAM_BASERECALIBRATOR_SPARK } from '../../subworkflows/local/bam_baserecalibrator_spark/main'
include { BAM_BASERECALIBRATOR } from '../../subworkflows/local/bam_baserecalibrator/main'
include { BAM_BASERECALIBRATOR_SPARK } from '../../subworkflows/local/bam_baserecalibrator_spark/main'

// Create recalibrated cram files to use for variant calling (+QC)
include { BAM_APPLYBQSR } from '../../subworkflows/local/bam_applybqsr/main'
include { BAM_APPLYBQSR_SPARK } from '../../subworkflows/local/bam_applybqsr_spark/main'
include { BAM_APPLYBQSR } from '../../subworkflows/local/bam_applybqsr/main'
include { BAM_APPLYBQSR_SPARK } from '../../subworkflows/local/bam_applybqsr_spark/main'

// Variant calling on a single normal sample
include { BAM_VARIANT_CALLING_GERMLINE_ALL } from '../../subworkflows/local/bam_variant_calling_germline_all/main'
include { BAM_VARIANT_CALLING_GERMLINE_ALL } from '../../subworkflows/local/bam_variant_calling_germline_all/main'

// Variant calling on a single tumor sample
include { BAM_VARIANT_CALLING_TUMOR_ONLY_ALL } from '../../subworkflows/local/bam_variant_calling_tumor_only_all/main'
include { BAM_VARIANT_CALLING_TUMOR_ONLY_ALL } from '../../subworkflows/local/bam_variant_calling_tumor_only_all/main'

// Variant calling on tumor/normal pair
include { BAM_VARIANT_CALLING_SOMATIC_ALL } from '../../subworkflows/local/bam_variant_calling_somatic_all/main'
include { BAM_VARIANT_CALLING_SOMATIC_ALL } from '../../subworkflows/local/bam_variant_calling_somatic_all/main'

// POST VARIANTCALLING: e.g. merging
include { POST_VARIANTCALLING } from '../../subworkflows/local/post_variantcalling/main'
include { POST_VARIANTCALLING } from '../../subworkflows/local/post_variantcalling/main'

// QC on VCF files
include { VCF_QC_BCFTOOLS_VCFTOOLS } from '../../subworkflows/local/vcf_qc_bcftools_vcftools/main'
include { VCF_QC_BCFTOOLS_VCFTOOLS } from '../../subworkflows/local/vcf_qc_bcftools_vcftools/main'

// Annotation
include { VCF_ANNOTATE_ALL } from '../../subworkflows/local/vcf_annotate_all/main'
include { VCF_ANNOTATE_ALL } from '../../subworkflows/local/vcf_annotate_all/main'

// MULTIQC
include { MULTIQC } from '../../modules/nf-core/multiqc/main'
include { MULTIQC } from '../../modules/nf-core/multiqc/main'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -164,13 +164,19 @@ workflow SAREK {
fastq_gz = input_sample_type.fastq_gz.map { meta, files -> addReadgroupToMeta(meta, files) }

// Just one fastq.gz.spring-file with both R1 and R2
fastq_gz_pair_from_spring = SPRING_DECOMPRESS_TO_FQ_PAIR(input_sample_type.one_fastq_gz_spring)
fastq_gz_pair_from_spring = SPRING_DECOMPRESS_TO_FQ_PAIR(input_sample_type.one_fastq_gz_spring, false)

one_fastq_gz_from_spring = fastq_gz_pair_from_spring.fastq.map { meta, files -> addReadgroupToMeta(meta, files) }

// Two fastq.gz.spring-files - one for R1 and one for R2
r1_fastq_gz_from_spring = SPRING_DECOMPRESS_TO_R1_FQ_PAIR(input_sample_type.two_fastq_gz_spring.map{ meta, files -> [meta, files[0] ]})
r2_fastq_gz_from_spring = SPRING_DECOMPRESS_TO_R2_FQ_PAIR(input_sample_type.two_fastq_gz_spring.map{ meta, files -> [meta, files[1] ]})
r1_fastq_gz_from_spring = SPRING_DECOMPRESS_TO_R1_FQ(input_sample_type.two_fastq_gz_spring.map{ meta, files ->
[meta, files[0] ]},
true // write_one_fastq_gz
)
r2_fastq_gz_from_spring = SPRING_DECOMPRESS_TO_R2_FQ(input_sample_type.two_fastq_gz_spring.map{ meta, files ->
[meta, files[1] ]},
true // write_one_fastq_gz
)

two_fastq_gz_from_spring = r1_fastq_gz_from_spring.fastq.join(r2_fastq_gz_from_spring.fastq).map{ meta, fastq_1, fastq_2 -> [meta, [fastq_1, fastq_2]]}

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