nf-core の workflow を CWL に移植する

やっていくぞ

まずはnfで動かします

pull して

run して

log を見る

wfで使ったコンテナとコマンドが知りたいので process hash, container, script を指定

code:nextflow

$ nextflow pull nf-core/viralrecon

$ nextflow run nf-core/viralrecon -profile test_nanopore,docker --outdir test_nanopore -with-dag flow.html

$ nextflow log

TIMESTAMP DURATION RUN NAME STATUS REVISION ID SESSION ID COMMAND

2022-08-30 16:43:53 9m 34s nauseous_poincare OK 3ee1fe98fd f9a76113-6a5e-4d31-97c0-f2c9e30dfeb7 nextflow run nf-core/viralrecon -profile test_nanopore,docker --outdir test_nanopore

2022-08-30 16:58:30 30.9s grave_edison ERR 3ee1fe98fd f04246f2-7d2e-449c-b233-c4e520d16ff2 nextflow run nf-core/viralrecon -profile test_nanopore,docker --outdir test_nanopore -stub-run

2022-08-30 17:12:02 4m 20s condescending_torvalds OK 3ee1fe98fd 98a0e65d-a185-4e77-a79c-31beddeaf9ed nextflow run nf-core/viralrecon -profile test_nanopore,docker --outdir test_nanopore -with-dag flow.html

2022-08-30 17:49:04 4m 35s pedantic_nightingale OK 3ee1fe98fd 336cf0a5-62b5-443c-9a3d-042f880e7c78 nextflow run nf-core/viralrecon -profile test_nanopore,docker --outdir test_nanopore -with-dag

$ nextflow log -l

$ nextflow log pedantic_nightingale -f hash,container,script

ここから吐き出されたスクリプト群を泥臭く変換していく

残りのスクリプトは改行を殺して複数コマンドは && で繋いでやる

複数のサンプルに対して同じ処理を行う部分が多いので sort してやる

コマンドをダブルクオートで括る

謎の python script 直打ちはどうでもよさそうなので削除

etc.

そうするとこれが

code:log.raw

ac/2a9e11 quay.io/biocontainers/python:3.9--1

check_samplesheet.py \

samplesheet_test_nanopore.csv \

samplesheet.valid.csv \

--platform nanopore

cat <<-END_VERSIONS > versions.yml

"NFCORE_VIRALRECON:NANOPORE:INPUT_CHECK:SAMPLESHEET_CHECK":

python: $(python --version | sed 's/Python //g')

END_VERSIONS

d5/70321f quay.io/biocontainers/python:3.9--1

collapse_primer_bed.py \

--left_primer_suffix _LEFT \

--right_primer_suffix _RIGHT \

nCoV-2019.primer.bed \

nCoV-2019.primer.collapsed.bed

cat <<-END_VERSIONS > versions.yml

"NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:COLLAPSE_PRIMERS":

python: $(python --version | sed 's/Python //g')

END_VERSIONS

f1/ebc3d2 ubuntu:20.04

gunzip \

-f \

\

GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz

cat <<-END_VERSIONS > versions.yml

"NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:GUNZIP_GFF":

gunzip: $(echo $(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*$//')

END_VERSIONS

32/983449 quay.io/biocontainers/samtools:1.15.1--h1170115_0

samtools faidx nCoV-2019.reference.fasta

cut -f 1,2 nCoV-2019.reference.fasta.fai > nCoV-2019.reference.fasta.sizes

cat <<-END_VERSIONS > versions.yml

"NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:CUSTOM_GETCHROMSIZES":

custom: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')

END_VERSIONS

こうなる

code:log_sorted

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "artic guppyplex --min-length 400 --max-length 700 --directory barcode01 --output SAMPLE_01.fastq && pigz -p 2 *.fastq"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "artic guppyplex --min-length 400 --max-length 700 --directory barcode02 --output SAMPLE_02.fastq && pigz -p 2 *.fastq"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "artic guppyplex --min-length 400 --max-length 700 --directory barcode03 --output SAMPLE_03.fastq && pigz -p 2 *.fastq"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "artic guppyplex --min-length 400 --max-length 700 --directory barcode04 --output SAMPLE_04.fastq && pigz -p 2 *.fastq"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "artic guppyplex --min-length 400 --max-length 700 --directory barcode05 --output SAMPLE_05.fastq && pigz -p 2 *.fastq"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "artic guppyplex --min-length 400 --max-length 700 --directory barcode06 --output SAMPLE_06.fastq && pigz -p 2 *.fastq"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "artic guppyplex --min-length 400 --max-length 700 --directory barcode07 --output SAMPLE_07.fastq && pigz -p 2 *.fastq"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "artic guppyplex --min-length 400 --max-length 700 --directory barcode08 --output SAMPLE_08.fastq && pigz -p 2 *.fastq"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "artic guppyplex --min-length 400 --max-length 700 --directory barcode09 --output SAMPLE_09.fastq && pigz -p 2 *.fastq"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin && artic minion --normalise 500 --minimap2 --threads 2 --read-file SAMPLE_01.fastq.gz --scheme-directory ./primer-schemes --scheme-version 3 --fast5-directory fast5_pass --sequencing-summary sequencing_summary.txt nCoV-2019 SAMPLE_01"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin && artic minion --normalise 500 --minimap2 --threads 2 --read-file SAMPLE_02.fastq.gz --scheme-directory ./primer-schemes --scheme-version 3 --fast5-directory fast5_pass --sequencing-summary sequencing_summary.txt nCoV-2019 SAMPLE_02"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin && artic minion --normalise 500 --minimap2 --threads 2 --read-file SAMPLE_03.fastq.gz --scheme-directory ./primer-schemes --scheme-version 3 --fast5-directory fast5_pass --sequencing-summary sequencing_summary.txt nCoV-2019 SAMPLE_03"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin && artic minion --normalise 500 --minimap2 --threads 2 --read-file SAMPLE_04.fastq.gz --scheme-directory ./primer-schemes --scheme-version 3 --fast5-directory fast5_pass --sequencing-summary sequencing_summary.txt nCoV-2019 SAMPLE_04"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin && artic minion --normalise 500 --minimap2 --threads 2 --read-file SAMPLE_05.fastq.gz --scheme-directory ./primer-schemes --scheme-version 3 --fast5-directory fast5_pass --sequencing-summary sequencing_summary.txt nCoV-2019 SAMPLE_05"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin && artic minion --normalise 500 --minimap2 --threads 2 --read-file SAMPLE_06.fastq.gz --scheme-directory ./primer-schemes --scheme-version 3 --fast5-directory fast5_pass --sequencing-summary sequencing_summary.txt nCoV-2019 SAMPLE_06"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin && artic minion --normalise 500 --minimap2 --threads 2 --read-file SAMPLE_07.fastq.gz --scheme-directory ./primer-schemes --scheme-version 3 --fast5-directory fast5_pass --sequencing-summary sequencing_summary.txt nCoV-2019 SAMPLE_07"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin && artic minion --normalise 500 --minimap2 --threads 2 --read-file SAMPLE_08.fastq.gz --scheme-directory ./primer-schemes --scheme-version 3 --fast5-directory fast5_pass --sequencing-summary sequencing_summary.txt nCoV-2019 SAMPLE_08"

-c quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0 "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin && artic minion --normalise 500 --minimap2 --threads 2 --read-file SAMPLE_09.fastq.gz --scheme-directory ./primer-schemes --scheme-version 3 --fast5-directory fast5_pass --sequencing-summary sequencing_summary.txt nCoV-2019 SAMPLE_09"

これがまあまあ大変である