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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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65 changes: 41 additions & 24 deletions tasks/quality_control/basic_statistics/task_fastq_scan.wdl
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Original file line number Diff line number Diff line change
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
}
}
1 change: 0 additions & 1 deletion tests/config/environment.yml
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Original file line number Diff line number Diff line change
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
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
Expand Down
5 changes: 2 additions & 3 deletions tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml
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Expand Up @@ -56,19 +56,18 @@
md5sum: d41d8cd98f00b204e9800998ecf8427e
# fastq scan raw
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/command
md5sum: 56f66a4ef82d3ae03c17db6a26f59528
md5sum: f96c3103490fff3560fc930a84bd459d
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/inputs.json
contains: ["read1", "illumina_se"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/outputs.json
contains: ["fastq_scan_se", "pipeline_date", "read1_seq"]
contains: ["fastq_scan_se", "read1_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
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/task.log
contains: ["wdl", "theiacov_illumina_se", "fastq_scan_raw", "done"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/ERR6319327_fastq-scan.json
md5sum: 66b2f7c60b74de654f590d77bdd2231e
- 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: 87f1a9ed69127009aa0c173cd74c9d31
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/VERSION
Expand Down
10 changes: 4 additions & 6 deletions tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
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Expand Up @@ -416,22 +416,21 @@
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/inputs.json
contains: ["read", "fastq"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/outputs.json
contains: ["read", "fastq", "fastq_scan_report"]
contains: ["read", "fastq", "fastq_scan_json"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stderr.txt
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stderr.txt.offset
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stdout.txt
contains: ["fastq", "qc_stats", "read_lengths"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/task.log
contains: ["wdl", "theiaprok_illumina_pe", "fastq_scan_clean", "done"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/DATE
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/READ1_SEQS
md5sum: 5fcafec683df465a99878ceaffe8a294
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/READ2_SEQS
md5sum: 5fcafec683df465a99878ceaffe8a294
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/READ_PAIRS
md5sum: 5fcafec683df465a99878ceaffe8a294
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/VERSION
md5sum: 8e4e9cdfbacc9021a3175ccbbbde002b
md5sum: a59bb42644e35c09b8fa8087156fa4c2
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/_miniwdl_inputs/0/test_1.clean.fastq.gz
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/_miniwdl_inputs/0/test_2.clean.fastq.gz
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/test_1.clean_fastq-scan.json
Expand All @@ -443,14 +442,13 @@
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/inputs.json
contains: ["read", "fastq"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/outputs.json
contains: ["read", "fastq", "fastq_scan_report"]
contains: ["read", "fastq", "fastq_scan_json"]
- 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
contains: ["fastq", "qc_stats", "read_lengths"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/task.log
contains: ["wdl", "theiaprok_illumina_pe", "fastq_scan_raw", "done"]
- 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: 75fa2f47fecb5dec8d244366881e76ec
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/READ2_SEQS
Expand All @@ -462,7 +460,7 @@
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/SRR2838702_R2_fastq-scan.json
md5sum: e81f34050c11995771de79182f06d793
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/VERSION
md5sum: 8e4e9cdfbacc9021a3175ccbbbde002b
md5sum: a59bb42644e35c09b8fa8087156fa4c2
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/_miniwdl_inputs/0/SRR2838702_R1.fastq.gz
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/_miniwdl_inputs/0/SRR2838702_R2.fastq.gz
- path: miniwdl_run/call-read_QC_trim/call-trimmomatic_pe/command
Expand Down
12 changes: 5 additions & 7 deletions tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
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Expand Up @@ -400,18 +400,17 @@
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/inputs.json
contains: ["read", "fastq"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/outputs.json
contains: ["read", "fastq", "fastq_scan_report"]
contains: ["read", "fastq", "fastq_scan_json"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stderr.txt
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stderr.txt.offset
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stdout.txt
contains: ["fastq", "qc_stats", "read_lengths"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/task.log
contains: ["wdl", "theiaprok_illumina_se", "fastq_scan_clean", "done"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/DATE
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/READ1_SEQS
md5sum: 499f7af0d267a13f5523ec9a60ec46e3
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/VERSION
md5sum: 8e4e9cdfbacc9021a3175ccbbbde002b
md5sum: a59bb42644e35c09b8fa8087156fa4c2
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/_miniwdl_inputs/0/test_1.clean.fastq.gz
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/test_1.clean_fastq-scan.json
md5sum: eb30273b3f19578fec5360da8b255e28
Expand All @@ -420,20 +419,19 @@
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/inputs.json
contains: ["read", "fastq"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/outputs.json
contains: ["read", "fastq", "fastq_scan_report"]
contains: ["read", "fastq", "fastq_scan_json"]
- 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
contains: ["fastq", "qc_stats", "read_lengths"]
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/task.log
contains: ["wdl", "theiaprok_illumina_se", "fastq_scan_raw", "done"]
- 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: 75fa2f47fecb5dec8d244366881e76ec
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/SRR2838702_R1_fastq-scan.json
md5sum: c4a64c8fd27fa357206e0d41b74866e2
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/VERSION
md5sum: 8e4e9cdfbacc9021a3175ccbbbde002b
md5sum: a59bb42644e35c09b8fa8087156fa4c2
- path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/_miniwdl_inputs/0/SRR2838702_R1.fastq.gz
- path: miniwdl_run/call-read_QC_trim/call-trimmomatic_se/command
md5sum: a317f1a2182fe1a3b26812b54eff088e
Expand Down Expand Up @@ -598,6 +596,6 @@
- path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
md5sum: ea5cff6eff8c2c42046cf2eae6f16b6f
- path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl
md5sum: d11bfe33fdd96eab28892be5a01c1c7d
md5sum: a7ef5a7a38dd60ff2edf699ae6808ebb
- path: miniwdl_run/workflow.log
contains: ["wdl", "theiaprok_illumina_se", "NOTICE", "done"]
4 changes: 4 additions & 0 deletions workflows/freyja/wf_freyja_fastq.wdl
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Expand Up @@ -116,10 +116,14 @@ workflow freyja_fastq {
String fastq_scan_num_reads_raw1 = select_first([read_QC_trim_pe.fastq_scan_raw1, read_QC_trim_se.fastq_scan_raw1, ""])
Int? fastq_scan_num_reads_raw2 = read_QC_trim_pe.fastq_scan_raw2
String? fastq_scan_num_reads_raw_pairs = read_QC_trim_pe.fastq_scan_raw_pairs
String fastq_scan_raw1_json = select_first([read_QC_trim_pe.fastq_scan_raw1_json, read_QC_trim_se.fastq_scan_raw1_json, ""])
File? fastq_scan_raw2_json = read_QC_trim_pe.fastq_scan_raw2_json
String fastq_scan_version = select_first([read_QC_trim_pe.fastq_scan_version, read_QC_trim_se.fastq_scan_version, ""])
String fastq_scan_num_reads_clean1 = select_first([read_QC_trim_pe.fastq_scan_clean1, read_QC_trim_se.fastq_scan_clean1, ""])
Int? fastq_scan_num_reads_clean2 = read_QC_trim_pe.fastq_scan_clean2
String? fastq_scan_num_reads_clean_pairs = read_QC_trim_pe.fastq_scan_clean_pairs
String fastq_scan_clean1_json = select_first([read_QC_trim_pe.fastq_scan_clean1_json, read_QC_trim_se.fastq_scan_clean1_json, ""])
File? fastq_scan_clean2_json = read_QC_trim_pe.fastq_scan_clean2_json
# Read QC - fastqc outputs - Illumina PE and SE
String fastqc_num_reads_raw1 = select_first([read_QC_trim_pe.fastqc_raw1, read_QC_trim_se.fastqc_raw1, ""])
Int? fastqc_num_reads_raw2 = read_QC_trim_pe.fastqc_raw2
Expand Down
4 changes: 4 additions & 0 deletions workflows/theiacov/wf_theiacov_illumina_pe.wdl
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Expand Up @@ -260,6 +260,10 @@ workflow theiacov_illumina_pe {
Int? fastq_scan_num_reads_clean1 = read_QC_trim.fastq_scan_clean1
Int? fastq_scan_num_reads_clean2 = read_QC_trim.fastq_scan_clean2
String? fastq_scan_num_reads_clean_pairs = read_QC_trim.fastq_scan_clean_pairs
File? fastq_scan_raw1_json = read_QC_trim.fastq_scan_raw1_json
File? fastq_scan_raw2_json = read_QC_trim.fastq_scan_raw2_json
File? fastq_scan_clean1_json = read_QC_trim.fastq_scan_clean1_json
File? fastq_scan_clean2_json = read_QC_trim.fastq_scan_clean2_json
# Read QC - fastqc outputs
Int? fastqc_num_reads_raw1 = read_QC_trim.fastqc_raw1
Int? fastqc_num_reads_raw2 = read_QC_trim.fastqc_raw2
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2 changes: 2 additions & 0 deletions workflows/theiacov/wf_theiacov_illumina_se.wdl
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Expand Up @@ -215,6 +215,8 @@ workflow theiacov_illumina_se {
Int? fastq_scan_num_reads_raw1 = read_QC_trim.fastq_scan_raw1
String? fastq_scan_version = read_QC_trim.fastq_scan_version
Int? fastq_scan_num_reads_clean1 = read_QC_trim.fastq_scan_clean1
File? fastq_scan_raw1_json = read_QC_trim.fastq_scan_raw1_json
File? fastq_scan_clean1_json = read_QC_trim.fastq_scan_clean1_json
# Read QC - fastqc outputs
Int? fastqc_num_reads_raw1 = read_QC_trim.fastqc_raw1
Int? fastqc_num_reads_clean1 = read_QC_trim.fastqc_clean1
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4 changes: 4 additions & 0 deletions workflows/utilities/wf_read_QC_trim_pe.wdl
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Expand Up @@ -174,6 +174,10 @@ workflow read_QC_trim_pe {
String? fastq_scan_clean_pairs = fastq_scan_clean.read_pairs
String? fastq_scan_version = fastq_scan_raw.version
String? fastq_scan_docker = fastq_scan_raw.fastq_scan_docker
File? fastq_scan_raw1_json = fastq_scan_raw.read1_fastq_scan_json
File? fastq_scan_raw2_json = fastq_scan_raw.read2_fastq_scan_json
File? fastq_scan_clean1_json = fastq_scan_clean.read1_fastq_scan_json
File? fastq_scan_clean2_json = fastq_scan_clean.read2_fastq_scan_json

# fastqc
Int? fastqc_raw1 = fastqc_raw.read1_seq
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2 changes: 2 additions & 0 deletions workflows/utilities/wf_read_QC_trim_se.wdl
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Expand Up @@ -149,6 +149,8 @@ workflow read_QC_trim_se {
Int? fastq_scan_clean1 = fastq_scan_clean.read1_seq
String? fastq_scan_version = fastq_scan_raw.version
String? fastq_scan_docker = fastq_scan_raw.fastq_scan_docker
File? fastq_scan_raw1_json = fastq_scan_raw.fastq_scan_json
File? fastq_scan_clean1_json = fastq_scan_clean.fastq_scan_json

# fastqc
Int? fastqc_raw1 = fastqc_raw.read1_seq
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