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Proposal: Rename output from fastp module (#1802)
* Rename output from fastp module * UPdate tests * fix alignment * prettier * Update modules/fastp/main.nf Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> * apply review suggestion -sf * typo * update md5 * update md5 * try with human data * revert, human data also doesn't work * use contains instead Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
This commit is contained in:
FriederikeHanssen
GitHub
parent
1363130410
commit
9b51362a53
3 changed files with 34 additions and 34 deletions
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@ -13,7 +13,7 @@ process FASTP {
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val save_merged
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output:
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tuple val(meta), path('*.trim.fastq.gz') , optional:true, emit: reads
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tuple val(meta), path('*.fastp.fastq.gz') , optional:true, emit: reads
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tuple val(meta), path('*.json') , emit: json
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tuple val(meta), path('*.html') , emit: html
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tuple val(meta), path('*.log') , emit: log
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@ -31,10 +31,10 @@ process FASTP {
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if (meta.single_end) {
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def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
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"""
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[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
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[ ! -f ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
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fastp \\
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--in1 ${prefix}.fastq.gz \\
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--out1 ${prefix}.trim.fastq.gz \\
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--out1 ${prefix}.fastp.fastq.gz \\
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--thread $task.cpus \\
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--json ${prefix}.fastp.json \\
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--html ${prefix}.fastp.html \\
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@ -50,13 +50,13 @@ process FASTP {
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def fail_fastq = save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
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def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''
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"""
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[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
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[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
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[ ! -f ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz
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[ ! -f ${prefix}_2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_2.fastq.gz
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fastp \\
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--in1 ${prefix}_1.fastq.gz \\
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--in2 ${prefix}_2.fastq.gz \\
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--out1 ${prefix}_1.trim.fastq.gz \\
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--out2 ${prefix}_2.trim.fastq.gz \\
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--out1 ${prefix}_1.fastp.fastq.gz \\
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--out2 ${prefix}_2.fastp.fastq.gz \\
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--json ${prefix}.fastp.json \\
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--html ${prefix}.fastp.html \\
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$fail_fastq \\
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@ -38,7 +38,7 @@ output:
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- reads:
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type: file
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description: The trimmed/modified/unmerged fastq reads
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pattern: "*trim.fastq.gz"
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pattern: "*fastp.fastq.gz"
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- json:
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type: file
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description: Results in JSON format
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@ -1,23 +1,23 @@
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- name: fastp test_fastp_single_end
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command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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tags:
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- fastp
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files:
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- path: output/fastp/test.fastp.fastq.gz
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md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
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- path: output/fastp/test.fastp.html
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contains:
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- "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
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- "single end (151 cycles)"
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- path: output/fastp/test.fastp.json
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md5sum: 7ee735cefb67f549dc857eefb9e7f123
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- path: output/fastp/test.fastp.log
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contains:
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- "Q20 bases: 12922(92.9841%)"
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- "reads passed filter: 99"
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- path: output/fastp/test.trim.fastq.gz
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md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
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- path: output/fastp/test.fastp.json
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md5sum: a517ba37b17a342b5428f2c1f8fe3dd7
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- name: fastp test_fastp_paired_end
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command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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tags:
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- fastp
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files:
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@ -25,40 +25,40 @@
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contains:
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- "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
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- "The input has little adapter percentage (~0.000000%), probably it's trimmed before."
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- path: output/fastp/test.fastp.json
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contains:
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- '"passed_filter_reads": 198'
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- path: output/fastp/test.fastp.log
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contains:
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- "No adapter detected for read1"
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- "Q30 bases: 12281(88.3716%)"
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- path: output/fastp/test.fastp.json
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contains:
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- '"passed_filter_reads": 198'
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- path: output/fastp/test_1.trim.fastq.gz
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- path: output/fastp/test_1.fastp.fastq.gz
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md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
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- path: output/fastp/test_2.trim.fastq.gz
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- path: output/fastp/test_2.fastp.fastq.gz
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md5sum: 532b190fb4dc7b2277ee5cf1464e598c
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- name: fastp test_fastp_single_end_trim_fail
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command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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tags:
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- fastp
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files:
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- path: output/fastp/test.fail.fastq.gz
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md5sum: b57f2026eb259a0b0c0b3960c270258d
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- path: output/fastp/test.fastp.fastq.gz
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md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
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- path: output/fastp/test.fastp.html
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contains:
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- "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
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- "single end (151 cycles)"
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- path: output/fastp/test.fastp.json
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md5sum: feafc4181a2a61b4b52d9c2b59b419ad
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- path: output/fastp/test.fastp.log
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contains:
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- "Q20 bases: 12922(92.9841%)"
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- "reads passed filter: 99"
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- path: output/fastp/test.trim.fastq.gz
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md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
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- path: output/fastp/test.fastp.json
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md5sum: 4be682c727942a45fc4c8600c28694a8
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- path: output/fastp/test.fail.fastq.gz
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md5sum: b57f2026eb259a0b0c0b3960c270258d
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- name: fastp test_fastp_paired_end_trim_fail
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command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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tags:
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- fastp
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files:
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@ -73,17 +73,17 @@
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- path: output/fastp/test.fastp.json
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contains:
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- '"passed_filter_reads": 198'
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- path: output/fastp/test_1.trim.fastq.gz
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md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
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- path: output/fastp/test_2.trim.fastq.gz
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md5sum: 532b190fb4dc7b2277ee5cf1464e598c
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- path: output/fastp/test_1.fail.fastq.gz
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/fastp/test_1.fastp.fastq.gz
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md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
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- path: output/fastp/test_2.fail.fastq.gz
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md5sum: 72d0002841967676ac936d08746a9128
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- path: output/fastp/test_2.fastp.fastq.gz
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md5sum: 532b190fb4dc7b2277ee5cf1464e598c
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- name: fastp test_fastp_paired_end_merged
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command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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tags:
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- fastp
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files:
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@ -102,7 +102,7 @@
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- "total bases: 13683"
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- path: output/fastp/test.merged.fastq.gz
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md5sum: 4955ca2c899729b17bd526d2626a8d73
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- path: output/fastp/test_1.trim.fastq.gz
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- path: output/fastp/test_1.fastp.fastq.gz
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md5sum: 4a03721ee252b7c6e81e007550e6ab63
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- path: output/fastp/test_2.trim.fastq.gz
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- path: output/fastp/test_2.fastp.fastq.gz
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md5sum: 7a4ddf8485c147cd7aaf0d4f6cd57ace
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