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Chipseq updates #111

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Chipseq updates #111

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d3a1280
fix: Paired-end ChIP-Seq
adthrasher Sep 20, 2023
a7f0d6b
fix: missing samtools option
adthrasher Sep 20, 2023
cbb83af
docs: add clarifying meta and comments
adthrasher Sep 20, 2023
d98a1a9
chore: Bump SEAseq to latest release
adthrasher Sep 21, 2023
da5b3c1
feat: Add samtools fixmate
adthrasher Sep 21, 2023
a51216f
chore: reorder parameters
adthrasher Sep 21, 2023
40ef841
docs: apply suggestions from code review @afrantz
adthrasher Sep 26, 2023
685174b
chore: merge main
adthrasher Feb 7, 2025
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47 changes: 34 additions & 13 deletions workflows/chipseq/chipseq-standard.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,11 @@ import "../../tools/samtools.wdl"
import "../../tools/util.wdl"
import "../general/bam-to-fastqs.wdl" as b2fq
#@ except: LineWidth
import "https://raw.githubusercontent.com/stjude/seaseq/2.3/workflows/workflows/mapping.wdl" as seaseq_map
import "https://raw.githubusercontent.com/stjude/seaseq/3.1/workflows/tasks/samtools.wdl" as seaseq_samtools
#@ except: LineWidth
import "https://raw.githubusercontent.com/stjude/seaseq/3.0/workflows/tasks/samtools.wdl" as seaseq_samtools
import "https://raw.githubusercontent.com/stjude/seaseq/3.1/workflows/tasks/seaseq_util.wdl" as seaseq_util
#@ except: LineWidth
import "https://raw.githubusercontent.com/stjude/seaseq/3.0/workflows/tasks/seaseq_util.wdl" as seaseq_util
import "https://raw.githubusercontent.com/stjude/seaseq/3.1/workflows/workflows/mapping.wdl" as seaseq_map

workflow chipseq_standard {
meta {
Expand All @@ -31,6 +31,7 @@ workflow chipseq_standard {
parameter_meta {
bam: "Input BAM format file to realign with bowtie"
bowtie_indexes: "Database of v1 reference files for the bowtie aligner. Can be generated with https://github.com/stjude/seaseq/blob/master/workflows/tasks/bowtie.wdl. [*.ebwt]"
paired_end: "Is the data paired-end (true) or single-end (false)?"
excludelist: "Optional list of regions that will be excluded after reference alignment"
prefix: "Prefix for output files"
validate_input: "Run Picard ValidateSamFile on the input BAM"
Expand All @@ -43,6 +44,7 @@ workflow chipseq_standard {
Array[File] bowtie_indexes
File? excludelist
String prefix = basename(bam, ".bam")
Boolean paired_end = false
Boolean validate_input = true
Boolean use_all_cores = false
Int subsample_n_reads = -1
Expand Down Expand Up @@ -84,28 +86,36 @@ workflow chipseq_standard {
bam_index = samtools_index_input.bam_index,
}

scatter (pair in zip(bam_to_fastqs.read1s, get_read_groups.read_groups)){
scatter (tuple in zip(
zip(
bam_to_fastqs.read1s,
bam_to_fastqs.read2s
),
get_read_groups.read_groups)){
call seaseq_util.basicfastqstats as basic_stats { input:
fastqfile = pair.left
fastqfile = tuple.left.left
}
call seaseq_map.mapping as bowtie_single_end_mapping { input:
fastqfile = pair.left,
#@ except: LineWidth
call seaseq_map.mapping as bowtie_mapping { input:
fastqfile = tuple.left.left, # the FASTQ pair is the left of the first pair, then it is R1 = left, R2 = right in the nested pair
fastqfile_R2 = tuple.left.right,
index_files = bowtie_indexes,
metricsfile = basic_stats.metrics_out,
blacklist = excludelist,
paired_end,
}
File chosen_bam = select_first(
[
bowtie_single_end_mapping.bklist_bam,
bowtie_single_end_mapping.mkdup_bam,
bowtie_single_end_mapping.sorted_bam,
bowtie_mapping.bklist_bam,
bowtie_mapping.mkdup_bam,
bowtie_mapping.sorted_bam
]
)
call util.add_to_bam_header { input:
bam = chosen_bam,
additional_header = pair.right,
additional_header = tuple.right,
}
String rg_id_field = sub(sub(pair.right, ".*ID:", "ID:"), "\t.*", "")
String rg_id_field = sub(sub(tuple.right, ".*ID:", "ID:"), "\t.*", "")
String rg_id = sub(rg_id_field, "ID:", "")
call samtools.addreplacerg as single_end { input:
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Rename single_end to something else

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poke

bam = add_to_bam_header.reheadered_bam,
Expand Down Expand Up @@ -133,8 +143,19 @@ workflow chipseq_standard {
bam = markdup.mkdupbam,
use_all_cores,
}

#@ except: UnusedCall
call picard.validate_bam { input: bam = markdup.mkdupbam }
call picard.validate_bam { input:
bam = markdup.mkdupbam,
ignore_list = [
"MISSING_PLATFORM_VALUE",
"INVALID_PLATFORM_VALUE",
"INVALID_MAPPING_QUALITY",
"MATES_ARE_SAME_END",
"MISMATCH_FLAG_MATE_NEG_STRAND",
"MISMATCH_MATE_ALIGNMENT_START"
Comment on lines +151 to +156
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The first two seem "ok" to ignore. Less comfortable ignoring the last four. Are all these still being produced by seaseq?

],
}

call md5sum.compute_checksum { input:
file = markdup.mkdupbam,
Expand Down
1 change: 1 addition & 0 deletions workflows/general/bam-to-fastqs.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ workflow bam_to_fastqs {
bam,
use_all_cores,
}

scatter (split_bam in split.split_bams) {
call samtools.bam_to_fastq { input:
bam = split_bam,
Expand Down