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[TheiaCoV/TheiaProk/TheiaMeta/TheiaEuk/Freyja_FASTQ] fastq-scan updates & improvements. Adding JSON as wf output file #662

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merged 19 commits into from
Nov 8, 2024
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[TheiaCoV/TheiaProk/TheiaMeta/TheiaEuk/Freyja_FASTQ] fastq-scan updates & improvements. Adding JSON as wf output file #662

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e41ddbc
lots of updates to fastq_scan_pe task: upgrade to fastq-scan 1.0.1; r…
kapsakcj Oct 22, 2024
998c509
similar changes also made to fastq_scan_se task: updated docker image…
kapsakcj Oct 22, 2024
2074400
Merge remote-tracking branch 'origin/main' into cjk-fastq-scan-json-o…
kapsakcj Oct 28, 2024
e9bbe00
added fastq-scan JSON outputs to read_qc_trim_pe subwf and theiacov_i…
kapsakcj Oct 29, 2024
e13b381
update CI. also removed 'defaults' from conda channels used to instal…
kapsakcj Oct 29, 2024
318ff34
update CI for theiaprok_illumina_pe. should pass now
kapsakcj Oct 29, 2024
8555c3f
add 2 fastq-scan JSON outputs to theiacov_illumina_SE wf and read_qc_…
kapsakcj Oct 29, 2024
099d364
add fastq-scan-json outputs to freyja_fastq wf
kapsakcj Oct 29, 2024
44c4094
update theiacov and theiaprok SE CI
kapsakcj Oct 29, 2024
9685652
added 2 fastq-scan JSON outputs to theiacov_clearlabs wf; added 4 fas…
kapsakcj Oct 30, 2024
5f37276
update theiacov_clearlabs CI
kapsakcj Oct 30, 2024
55fbbde
added fastq-scan JSON outputs to export_taxon_tables task and added a…
kapsakcj Nov 4, 2024
0e12639
add fastq-scan json outputs to theiaprok_illumina PE and SE wfs
kapsakcj Nov 4, 2024
93be00c
added 4 fastq-scan JSON outputs to theiaeuk_illumina_pe wf
kapsakcj Nov 4, 2024
14999a0
Merge remote-tracking branch 'origin/main' into cjk-fastq-scan-json-o…
kapsakcj Nov 4, 2024
53b501b
export_taxon_tables task: added set -euo pipefail and removed bug cau…
kapsakcj Nov 4, 2024
967e0f6
update CI
kapsakcj Nov 4, 2024
8d2860b
update docs with new JSON outputs for freyja, theiacov wfs, theiaeuk,…
kapsakcj Nov 4, 2024
8203814
update CI for snippy_variants task
kapsakcj Nov 7, 2024
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4 changes: 4 additions & 0 deletions docs/workflows/genomic_characterization/freyja.md
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Expand Up @@ -327,12 +327,16 @@ The main output file used in subsequent Freyja workflows is found under the `fre
| bwa_version | String | Version of BWA used to map read data to the reference genome | PE, SE |
| fastp_html_report | File | The HTML report made with fastp | PE, SE |
| fastp_version | String | Version of fastp software used | PE, SE |
| fastq_scan_clean1_json | File | JSON file output from `fastq-scan` containing summary stats about clean forward read quality and length | PE, SE |
| fastq_scan_clean2_json | File | JSON file output from `fastq-scan` containing summary stats about clean reverse read quality and length | PE |
| fastq_scan_num_reads_clean_pairs | String | Number of clean read pairs | PE |
| fastq_scan_num_reads_clean1 | Int | Number of clean forward reads | PE, SE |
| fastq_scan_num_reads_clean2 | Int | Number of clean reverse reads | PE |
| fastq_scan_num_reads_raw_pairs | String | Number of raw read pairs | PE |
| fastq_scan_num_reads_raw1 | Int | Number of raw forward reads | PE, SE |
| fastq_scan_num_reads_raw2 | Int | Number of raw reverse reads | PE |
| fastq_scan_raw1_json | File | JSON file output from `fastq-scan` containing summary stats about raw forward read quality and length | PE, SE |
| fastq_scan_raw2_json | File | JSON file output from `fastq-scan` containing summary stats about raw reverse read quality and length | PE |
| fastq_scan_version | String | Version of fastq_scan used for read QC analysis | PE, SE |
| fastqc_clean1_html | File | Graphical visualization of clean forward read quality from fastqc to open in an internet browser | PE, SE |
| fastqc_clean2_html | File | Graphical visualization of clean reverse read quality from fastqc to open in an internet browser | PE |
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4 changes: 4 additions & 0 deletions docs/workflows/genomic_characterization/theiacov.md
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Expand Up @@ -1026,6 +1026,8 @@ All TheiaCoV Workflows (not TheiaCoV_FASTA_Batch)
| est_percent_gene_coverage_tsv | File | Percent coverage for each gene in the organism being analyzed (depending on the organism input) | CL, ONT, PE, SE |
| fastp_html_report | File | HTML report for fastp | PE, SE |
| fastp_version | String | Fastp version used | PE, SE |
| fastq_scan_clean1_json | File | JSON file output from `fastq-scan` containing summary stats about clean forward read quality and length | PE, SE, CL |
| fastq_scan_clean2_json | File | JSON file output from `fastq-scan` containing summary stats about clean reverse read quality and length | PE |
| fastq_scan_num_reads_clean_pairs | String | Number of paired reads after filtering as determined by fastq_scan | PE |
| fastq_scan_num_reads_clean1 | Int | Number of forward reads after filtering as determined by fastq_scan | CL, PE, SE |
| fastq_scan_num_reads_clean2 | Int | Number of reverse reads after filtering as determined by fastq_scan | PE |
Expand All @@ -1036,6 +1038,8 @@ All TheiaCoV Workflows (not TheiaCoV_FASTA_Batch)
| fastq_scan_r1_mean_q_raw | Float | Forward read mean quality value before quality trimming and adapter removal | |
| fastq_scan_r1_mean_readlength_clean | Float | Forward read mean read length value after quality trimming and adapter removal | |
| fastq_scan_r1_mean_readlength_raw | Float | Forward read mean read length value before quality trimming and adapter removal | |
| fastq_scan_raw1_json | File | JSON file output from `fastq-scan` containing summary stats about raw forward read quality and length | PE, SE, CL |
| fastq_scan_raw2_json | File | JSON file output from `fastq-scan` containing summary stats about raw reverse read quality and length | PE |
| fastq_scan_version | String | Version of fastq_scan used for read QC analysis | CL, PE, SE |
| fastqc_clean1_html | File | Graphical visualization of clean forward read quality from fastqc to open in an internet browser | PE, SE |
| fastqc_clean2_html | File | Graphical visualization of clean reverse read quality from fastqc to open in an internet browser | PE |
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4 changes: 4 additions & 0 deletions docs/workflows/genomic_characterization/theiaeuk.md
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Expand Up @@ -484,6 +484,10 @@ The TheiaEuk workflow automatically activates taxa-specific tasks after identifi
| cg_pipeline_report | File | TSV file of read metrics from raw reads, including average read length, number of reads, and estimated genome coverage |
| est_coverage_clean | Float | Estimated coverage calculated from clean reads and genome length |
| est_coverage_raw | Float | Estimated coverage calculated from raw reads and genome length |
| fastq_scan_clean1_json | File | JSON file output from `fastq-scan` containing summary stats about clean forward read quality and length |
| fastq_scan_clean2_json | File | JSON file output from `fastq-scan` containing summary stats about clean reverse read quality and length |
| fastq_scan_raw1_json | File | JSON file output from `fastq-scan` containing summary stats about raw forward read quality and length |
| fastq_scan_raw2_json | File | JSON file output from `fastq-scan` containing summary stats about raw reverse read quality and length |
| r1_mean_q_clean | Float | Mean quality score of clean forward reads |
| r1_mean_q_raw | Float | Mean quality score of raw forward reads |
| r2_mean_q_clean | Float | Mean quality score of clean reverse reads |
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4 changes: 4 additions & 0 deletions docs/workflows/genomic_characterization/theiameta.md
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Expand Up @@ -295,12 +295,16 @@ The TheiaMeta_Illumina_PE workflow processes Illumina paired-end (PE) reads ge
| fastp_html_report | File | Report file for fastp in HTML format |
| fastp_version | String | Version of fastp used |
| fastq_scan_docker | String | Docker image of fastq_scan |
| fastq_scan_clean1_json | File | JSON file output from `fastq-scan` containing summary stats about clean forward read quality and length |
| fastq_scan_clean2_json | File | JSON file output from `fastq-scan` containing summary stats about clean reverse read quality and length |
| fastq_scan_num_reads_clean_pairs | String | Number of read pairs after cleaning as calculated by fastq_scan |
| fastq_scan_num_reads_clean1 | Int | Number of forward reads after cleaning as calculated by fastq_scan |
| fastq_scan_num_reads_clean2 | Int | Number of reverse reads after cleaning as calculated by fastq_scan |
| fastq_scan_num_reads_raw_pairs | String | Number of input read pairs as calculated by fastq_scan |
| fastq_scan_num_reads_raw1 | Int | Number of input forward reads as calculated by fastq_scan |
| fastq_scan_num_reads_raw2 | Int | Number of input reserve reads as calculated by fastq_scan |
| fastq_scan_raw1_json | File | JSON file output from `fastq-scan` containing summary stats about raw forward read quality and length |
| fastq_scan_raw2_json | File | JSON file output from `fastq-scan` containing summary stats about raw reverse read quality and length |
| fastq_scan_version | String | fastq_scan version |
| fastqc_clean1_html | File | Graphical visualization of clean forward read quality from fastqc to open in an internet browser |
| fastqc_clean2_html | File | Graphical visualization of clean reverse read quality from fastqc to open in an internet browser |
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4 changes: 4 additions & 0 deletions docs/workflows/genomic_characterization/theiaprok.md
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Expand Up @@ -1704,12 +1704,16 @@ The TheiaProk workflows automatically activate taxa-specific sub-workflows after
| est_coverage_raw | Float | Estimated coverage calculated from raw reads and genome length | ONT, PE, SE |
| fastp_html_report | File | The HTML report made with fastp | PE, SE |
| fastp_version | String | Version of fastp software used | PE, SE |
| fastq_scan_clean1_json | File | JSON file output from `fastq-scan` containing summary stats about clean forward read quality and length | PE, SE |
| fastq_scan_clean2_json | File | JSON file output from `fastq-scan` containing summary stats about clean reverse read quality and length | PE |
| fastq_scan_num_reads_clean_pairs | String | Number of read pairs after cleaning as calculated by fastq_scan | PE |
| fastq_scan_num_reads_clean1 | Int | Number of forward reads after cleaning as calculated by fastq_scan | PE, SE |
| fastq_scan_num_reads_clean2 | Int | Number of reverse reads after cleaning as calculated by fastq_scan | PE |
| fastq_scan_num_reads_raw_pairs | String | Number of input read pairs calculated by fastq_scan | PE |
| fastq_scan_num_reads_raw1 | Int | Number of input forward reads calculated by fastq_scan | PE, SE |
| fastq_scan_num_reads_raw2 | Int | Number of input reverse reads calculated by fastq_scan | PE |
| fastq_scan_raw1_json | File | JSON file output from `fastq-scan` containing summary stats about raw forward read quality and length | PE, SE |
| fastq_scan_raw2_json | File | JSON file output from `fastq-scan` containing summary stats about raw reverse read quality and length | PE |
| fastq_scan_version | String | Version of fastq-scan software used | PE, SE |
| fastqc_clean1_html | File | Graphical visualization of clean forward read quality from fastqc to open in an internet browser | PE, SE |
| fastqc_clean2_html | File | Graphical visualization of clean reverse read quality from fastqc to open in an internet browser | PE |
Expand Down
65 changes: 41 additions & 24 deletions tasks/quality_control/basic_statistics/task_fastq_scan.wdl
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Expand Up @@ -6,14 +6,16 @@ task fastq_scan_pe {
File read2
String read1_name = basename(basename(basename(read1, ".gz"), ".fastq"), ".fq")
String read2_name = basename(basename(basename(read2, ".gz"), ".fastq"), ".fq")
Int disk_size = 100
String docker = "quay.io/biocontainers/fastq-scan:0.4.4--h7d875b9_1"
Int disk_size = 50
String docker = "us-docker.pkg.dev/general-theiagen/biocontainers/fastq-scan:1.0.1--h4ac6f70_3"
Int memory = 2
Int cpu = 2
Int cpu = 1
}
command <<<
# capture date and version
date | tee DATE
# exit task in case anything fails in one-liners or variables are unset
set -euo pipefail

# capture version
fastq-scan -v | tee VERSION

# set cat command based on compression
Expand All @@ -24,11 +26,21 @@ task fastq_scan_pe {
fi

# capture forward read stats
echo "DEBUG: running fastq-scan on $(basename ~{read1})"
eval "${cat_reads} ~{read1}" | fastq-scan | tee ~{read1_name}_fastq-scan.json
cat ~{read1_name}_fastq-scan.json | jq .qc_stats.read_total | tee READ1_SEQS
# using simple redirect so STDOUT is not confusing
jq .qc_stats.read_total ~{read1_name}_fastq-scan.json > READ1_SEQS
echo "DEBUG: number of reads in $(basename ~{read1}): $(cat READ1_SEQS)"
read1_seqs=$(cat READ1_SEQS)
echo

# capture reverse read stats
echo "DEBUG: running fastq-scan on $(basename ~{read2})"
eval "${cat_reads} ~{read2}" | fastq-scan | tee ~{read2_name}_fastq-scan.json
cat ~{read2_name}_fastq-scan.json | jq .qc_stats.read_total | tee READ2_SEQS

# using simple redirect so STDOUT is not confusing
jq .qc_stats.read_total ~{read2_name}_fastq-scan.json > READ2_SEQS
echo "DEBUG: number of reads in $(basename ~{read2}): $(cat READ2_SEQS)"
read2_seqs=$(cat READ2_SEQS)

# capture number of read pairs
Expand All @@ -37,26 +49,27 @@ task fastq_scan_pe {
else
read_pairs="Uneven pairs: R1=${read1_seqs}, R2=${read2_seqs}"
fi

echo $read_pairs | tee READ_PAIRS

# use simple redirect so STDOUT is not confusing
echo "$read_pairs" > READ_PAIRS
echo "DEBUG: number of read pairs: $(cat READ_PAIRS)"
>>>
output {
File read1_fastq_scan_report = "~{read1_name}_fastq-scan.json"
File read2_fastq_scan_report = "~{read2_name}_fastq-scan.json"
File read1_fastq_scan_json = "~{read1_name}_fastq-scan.json"
File read2_fastq_scan_json = "~{read2_name}_fastq-scan.json"
Int read1_seq = read_int("READ1_SEQS")
Int read2_seq = read_int("READ2_SEQS")
String read_pairs = read_string("READ_PAIRS")
String version = read_string("VERSION")
String pipeline_date = read_string("DATE")
String fastq_scan_docker = docker
}
runtime {
docker: docker
memory: memory + " GB"
cpu: cpu
disks: "local-disk " + disk_size + " SSD"
disk: disk_size + " GB" # TES
preemptible: 0
disk: disk_size + " GB"
preemptible: 1
maxRetries: 3
}
}
Expand All @@ -65,14 +78,16 @@ task fastq_scan_se {
input {
File read1
String read1_name = basename(basename(basename(read1, ".gz"), ".fastq"), ".fq")
Int disk_size = 100
Int disk_size = 50
Int memory = 2
Int cpu = 2
String docker = "quay.io/biocontainers/fastq-scan:0.4.4--h7d875b9_1"
Int cpu = 1
String docker = "us-docker.pkg.dev/general-theiagen/biocontainers/fastq-scan:1.0.1--h4ac6f70_3"
}
command <<<
# capture date and version
date | tee DATE
# exit task in case anything fails in one-liners or variables are unset
set -euo pipefail

# capture version
fastq-scan -v | tee VERSION

# set cat command based on compression
Expand All @@ -83,23 +98,25 @@ task fastq_scan_se {
fi

# capture forward read stats
echo "DEBUG: running fastq-scan on $(basename ~{read1})"
eval "${cat_reads} ~{read1}" | fastq-scan | tee ~{read1_name}_fastq-scan.json
cat ~{read1_name}_fastq-scan.json | jq .qc_stats.read_total | tee READ1_SEQS
# using simple redirect so STDOUT is not confusing
jq .qc_stats.read_total ~{read1_name}_fastq-scan.json > READ1_SEQS
echo "DEBUG: number of reads in $(basename ~{read1}): $(cat READ1_SEQS)"
>>>
output {
File fastq_scan_report = "~{read1_name}_fastq-scan.json"
File fastq_scan_json = "~{read1_name}_fastq-scan.json"
Int read1_seq = read_int("READ1_SEQS")
String version = read_string("VERSION")
String pipeline_date = read_string("DATE")
String fastq_scan_docker = docker
}
runtime {
docker: docker
memory: memory + " GB"
cpu: cpu
disks: "local-disk " + disk_size + " SSD"
disk: disk_size + " GB" # TES
preemptible: 0
disk: disk_size + " GB"
preemptible: 1
maxRetries: 3
}
}
13 changes: 11 additions & 2 deletions tasks/utilities/data_export/task_broad_terra_tools.wdl
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Expand Up @@ -35,6 +35,10 @@ task export_taxon_tables {
Int? num_reads_raw2
String? num_reads_raw_pairs
String? fastq_scan_version
File? fastq_scan_raw1_json
File? fastq_scan_raw2_json
File? fastq_scan_clean1_json
File? fastq_scan_clean2_json
Int? num_reads_clean1
Int? num_reads_clean2
String? num_reads_clean_pairs
Expand Down Expand Up @@ -390,7 +394,8 @@ task export_taxon_tables {
volatile: true
}
command <<<

set -euo pipefail

# capture taxon and corresponding table names from input taxon_tables
taxon_array=($(cut -f1 ~{taxon_tables} | tail +2))
echo "Taxon array: ${taxon_array[*]}"
Expand Down Expand Up @@ -446,6 +451,10 @@ task export_taxon_tables {
"num_reads_raw2": "~{num_reads_raw2}",
"num_reads_raw_pairs": "~{num_reads_raw_pairs}",
"fastq_scan_version": "~{fastq_scan_version}",
"fastq_scan_raw1_json": "~{fastq_scan_raw1_json}",
"fastq_scan_raw2_json": "~{fastq_scan_raw2_json}",
"fastq_scan_clean1_json": "~{fastq_scan_clean1_json}",
"fastq_scan_clean2_json": "~{fastq_scan_clean2_json}",
"num_reads_clean1": "~{num_reads_clean1}",
"num_reads_clean2": "~{num_reads_clean2}",
"num_reads_clean_pairs": "~{num_reads_clean_pairs}",
Expand Down Expand Up @@ -778,7 +787,7 @@ task export_taxon_tables {
"agrvate_version": "~{agrvate_version}",
"agrvate_docker": "~{agrvate_docker}",
"srst2_vibrio_detailed_tsv": "~{srst2_vibrio_detailed_tsv}",
"srst2_vibrio_version": "~{srst2_vibrio_version}",~
"srst2_vibrio_version": "~{srst2_vibrio_version}",
"srst2_vibrio_docker": "~{srst2_vibrio_docker}",
"srst2_vibrio_database": "~{srst2_vibrio_database}",
"srst2_vibrio_ctxA": "~{srst2_vibrio_ctxA}",
Expand Down
1 change: 0 additions & 1 deletion tests/config/environment.yml
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Expand Up @@ -2,7 +2,6 @@ name: pytest-env-CI
channels:
- conda-forge
- bioconda
- defaults
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We don't have more than 200 people in our organization, but most folks are moving away from using the defaults channel due to Anaconda updating their ToS: https://www.anaconda.com/blog/is-conda-free

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Thanks for picking up on this & making the quick fix!

dependencies:
- python >=3.7
- cromwell=86
Expand Down
10 changes: 4 additions & 6 deletions tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml
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Expand Up @@ -115,17 +115,16 @@
- path: miniwdl_run/call-fastq_scan_clean_reads/inputs.json
contains: ["read1", "clearlabs"]
- path: miniwdl_run/call-fastq_scan_clean_reads/outputs.json
contains: ["fastq_scan_se", "pipeline_date", "read1_seq"]
contains: ["fastq_scan_se", "read1_seq"]
- path: miniwdl_run/call-fastq_scan_clean_reads/stderr.txt
- path: miniwdl_run/call-fastq_scan_clean_reads/stderr.txt.offset
- path: miniwdl_run/call-fastq_scan_clean_reads/stdout.txt
- path: miniwdl_run/call-fastq_scan_clean_reads/task.log
contains: ["wdl", "theiacov_clearlabs", "fastq_scan_clean_reads", "done"]
- path: miniwdl_run/call-fastq_scan_clean_reads/work/DATE
- path: miniwdl_run/call-fastq_scan_clean_reads/work/READ1_SEQS
md5sum: 097e79b36919c8377c56088363e3d8b7
- path: miniwdl_run/call-fastq_scan_clean_reads/work/VERSION
md5sum: 8e4e9cdfbacc9021a3175ccbbbde002b
md5sum: a59bb42644e35c09b8fa8087156fa4c2
- path: miniwdl_run/call-fastq_scan_clean_reads/work/_miniwdl_inputs/0/clearlabs_R1_dehosted.fastq.gz
- path: miniwdl_run/call-fastq_scan_clean_reads/work/clearlabs_R1_dehosted_fastq-scan.json
md5sum: 869dd2e934c600bba35f30f08e2da7c9
Expand All @@ -134,17 +133,16 @@
- path: miniwdl_run/call-fastq_scan_raw_reads/inputs.json
contains: ["read1", "clearlabs"]
- path: miniwdl_run/call-fastq_scan_raw_reads/outputs.json
contains: ["fastq_scan_se", "pipeline_date", "read1_seq"]
contains: ["fastq_scan_se", "read1_seq"]
- path: miniwdl_run/call-fastq_scan_raw_reads/stderr.txt
- path: miniwdl_run/call-fastq_scan_raw_reads/stderr.txt.offset
- path: miniwdl_run/call-fastq_scan_raw_reads/stdout.txt
- path: miniwdl_run/call-fastq_scan_raw_reads/task.log
contains: ["wdl", "theiacov_clearlabs", "fastq_scan_raw_reads", "done"]
- path: miniwdl_run/call-fastq_scan_raw_reads/work/DATE
- path: miniwdl_run/call-fastq_scan_raw_reads/work/READ1_SEQS
md5sum: 097e79b36919c8377c56088363e3d8b7
- path: miniwdl_run/call-fastq_scan_raw_reads/work/VERSION
md5sum: 8e4e9cdfbacc9021a3175ccbbbde002b
md5sum: a59bb42644e35c09b8fa8087156fa4c2
- path: miniwdl_run/call-fastq_scan_raw_reads/work/_miniwdl_inputs/0/clearlabs.fastq.gz
- path: miniwdl_run/call-fastq_scan_raw_reads/work/clearlabs_fastq-scan.json
md5sum: 869dd2e934c600bba35f30f08e2da7c9
Expand Down
5 changes: 2 additions & 3 deletions tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml
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Expand Up @@ -60,11 +60,11 @@
md5sum: d41d8cd98f00b204e9800998ecf8427e
# fastq scan raw
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/command
md5sum: 9b2cc0107f1a90972482d7b3a658d242
md5sum: 56bcc1ba5d2a9c94f4704fc4b8e6b7ba
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/inputs.json
contains: ["read1", "read2", "illumina_pe"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/outputs.json
contains: ["fastq_scan_pe", "pipeline_date", "read1_seq", "read2_seq"]
contains: ["fastq_scan_pe", "read1_seq", "read2_seq"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stderr.txt
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stderr.txt.offset
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stdout.txt
Expand All @@ -74,7 +74,6 @@
md5sum: 2a77387b247176aa5fcc9aed228699c9
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/SRR13687078_2_fastq-scan.json
md5sum: d0eebdd4e14cf0a0b371fee1338474c9
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/DATE
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/READ1_SEQS
md5sum: 4e4a08422dbf7001fd09ad5126e13b44
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/READ2_SEQS
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