B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

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Introduction

** nf-core/airrflow ** is a bioinformatics best-practice pipeline to analyze B-cell or T-cell repertoire sequencing data. It makes use of the Immcantation toolset. The input data can be targeted amplicon bulk sequencing data of the V, D, J and C regions of the B/T-cell receptor with multiplex PCR or 5' RACE protocol, or assembled reads (bulk or single cell).

nf-core/airrflow overview

The pipeline is built using Nextflow , a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website .

Pipeline summary

nf-core/airrflow allows the end-to-end processing of BCR and TCR bulk and single cell targeted sequencing data. Several protocols are supported, please see the usage documenation for more details on the supported protocols.

nf-core/airrflow overview

QC and sequence assembly (bulk only)

Raw read quality control, adapter trimming and clipping ( Fastp ).
Filter sequences by base quality ( pRESTO FilterSeq ).
Mask amplicon primers ( pRESTO MaskPrimers ).
Pair read mates ( pRESTO PairSeq ).
For UMI-based sequencing:
- Cluster sequences according to similarity (optional for insufficient UMI diversity) ( pRESTO ClusterSets ).
- Build consensus of sequences with the same UMI barcode ( pRESTO BuildConsensus ).
Assemble R1 and R2 read mates ( pRESTO AssemblePairs ).
Remove and annotate read duplicates ( pRESTO CollapseSeq ).
Filter out sequences that do not have at least 2 duplicates ( pRESTO SplitSeq ).

V(D)J annotation and filtering (bulk and single-cell)

Assign gene segments with IgBlast using the IMGT database ( Change-O AssignGenes ).
Annotate alignments in AIRR format ( Change-O MakeDB )
Filter by alignment quality (locus matching v_call chain, min 200 informative positions, max 10% N nucleotides)
Filter productive sequences ( Change-O ParseDB split )
Filter junction length multiple of 3
Annotate metadata ( EnchantR )

QC filtering (bulk and single-cell)

Bulk sequencing filtering:
- Remove chimeric sequences (optional) ( SHazaM , EnchantR )
- Detect cross-contamination (optional) ( EnchantR )
- Collapse duplicates ( Alakazam , EnchantR )
Single-cell QC filtering ( EnchantR )
- Remove cells without heavy chains.
- Remove cells with multiple heavy chains.
- Remove sequences in different samples that share the same cell_id and nucleotide sequence.
- Modify cell_id s to ensure they are unique in the project.

Clonal analysis (bulk and single-cell)

Find threshold for clone definition ( SHazaM , EnchantR ).
Create germlines and define clones, repertoire analysis ( Change-O , EnchantR ).
Build lineage trees ( SCOPer , IgphyML , EnchantR ).

Repertoire analysis and reporting

Custom repertoire analysis pipeline report ( Alakazam ).
Aggregate QC reports ( MultiQC ).

Usage

Note If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, ensure that the pipeline tests run on your infrastructure:

nextflow run nf-core/airrflow -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute> --outdir <OUTDIR>

To run on your data, prepare a tab-separated samplesheet with your input data. Depending on the input data type (bulk or single-cell, raw reads or assembled reads) the input samplesheet will vary. Please follow the documentation on samplesheets for more details. An example samplesheet for running the pipeline on raw BCR / TCR sequencing data looks as follows:

sample_id	filename_R1	filename_R2	filename_I1	subject_id	species	pcr_target_locus	tissue	sex	age	biomaterial_provider	single_cell	intervention	collection_time_point_relative	cell_subset
sample01	sample1_S8_L001_R1_001.fastq.gz	sample1_S8_L001_R2_001.fastq.gz	sample1_S8_L001_I1_001.fastq.gz	Subject02	human	IG	blood	NA	53	sequencing_facility	FALSE	Drug_treatment	Baseline	plasmablasts
sample02	sample2_S8_L001_R1_001.fastq.gz	sample2_S8_L001_R2_001.fastq.gz	sample2_S8_L001_I1_001.fastq.gz	Subject02	human	TR	blood	female	78	sequencing_facility	FALSE	Drug_treatment	Baseline	plasmablasts

Each row represents a sample with fastq files (paired-end).

A typical command to run the pipeline is:

nextflow run nf-core/airrflow \
-profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
--input samplesheet.tsv \
--library_generation_method specific_pcr_umi \
--cprimers CPrimers.fasta \
--vprimers VPrimers.fasta \
--umi_length 12 \
--max_memory 8.GB \
--max_cpus 8 \
--outdir ./results

Warning: Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters ; see docs .

For more details, please refer to the usage documentation and the parameter documentation .

Pipeline output

To see the the results of a test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation .

Credits

nf-core/airrflow was written by Gisela Gabernet , Susanna Marquez , Alexander Peltzer and Simon Heumos .

Further contributors to the pipeline are:

@dladd

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines .

For further information or help, don't hesitate to get in touch on the Slack #airrflow channel (you can join with this invite ).

Citations

If you use nf-core/airrflow for your analysis, please cite it using the following DOI: 10.5281/zenodo.2642009

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x .

Code Snippets

"""
execute_report.R --report_file ${repertoire_report}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    alakazam: \$(Rscript -e "library(alakazam); cat(paste(packageVersion('alakazam'), collapse='.'))")
    shazam: \$(Rscript -e "library(shazam); cat(paste(packageVersion('shazam'), collapse='.'))")
    stringr: \$(Rscript -e "library(stringr); cat(paste(packageVersion('stringr'), collapse='.'))")
    dplyr: \$(Rscript -e "library(dplyr); cat(paste(packageVersion('dplyr'), collapse='.'))")
    knitr: \$(Rscript -e "library(knitr); cat(paste(packageVersion('knitr'), collapse='.'))")
    R: \$(echo \$(R --version 2>&1) | awk -F' '  '{print \$3}')
END_VERSIONS
"""

NextFlow shazam From line 27 of airrflow_report/airrflow_report.nf

"""
AssignGenes.py igblast -s $reads -b $igblast --organism $meta.species --loci ${meta.locus.toLowerCase()} $args --nproc $task.cpus --outname $meta.id > ${meta.id}_changeo_assigngenes_command_log.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    igblastn: \$( igblastn -version | grep -o "igblast[0-9\\. ]\\+" | grep -o "[0-9\\. ]\\+" )
    changeo: \$( AssignGenes.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow IgBLAST changeo From line 23 of changeo/changeo_assigngenes.nf

"""
ConvertDb.py fasta -d $tab $args > ${meta.id}_convertdb_command_log.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    igblastn: \$( igblastn -version | grep -o "igblast[0-9\\. ]\\+" | grep -o "[0-9\\. ]\\+" )
    changeo: \$( ConvertDb.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow IgBLAST changeo From line 22 of changeo/changeo_convertdb_fasta.nf

"""
CreateGermlines.py -d ${tab} \\
-r ${imgt_base}/${meta.species}/vdj/ \\
-g dmask --format airr \\
--log ${meta.id}.log --outname ${meta.id} $args > ${meta.id}_create-germlines_command_log.txt
ParseLog.py -l ${meta.id}.log -f ID V_CALL D_CALL J_CALL

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    igblastn: \$( igblastn -version | grep -o "igblast[0-9\\. ]\\+" | grep -o "[0-9\\. ]\\+" )
    changeo: \$( CreateGermlines.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow airr IgBLAST changeo From line 23 of changeo/changeo_creategermlines.nf

"""
MakeDb.py igblast -i $igblast -s $reads -r \\
${imgt_base}/${meta.species.toLowerCase()}/vdj/ \\
$args \\
--outname ${meta.id} > ${meta.id}_makedb_command_log.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    igblastn: \$( igblastn -version | grep -o "igblast[0-9\\. ]\\+" | grep -o "[0-9\\. ]\\+" )
    changeo: \$( MakeDb.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow IgBLAST changeo From line 24 of changeo/changeo_makedb.nf

"""
ParseDb.py split -d $tab -f productive --outname ${meta.id} > ${meta.id}_split_command_log.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    changeo: \$( ParseDb.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow changeo From line 21 of changeo/changeo_parsedb_split.nf

"""
echo "${tabs.join('\n')}" > tabs.txt
Rscript -e "enchantr::enchantr_report('collapse_duplicates', \\
    report_params=list('input'='tabs.txt',\\
    'collapseby'='${params.collapseby}',\\
    'outdir'=getwd(),\\
    'nproc'=${task.cpus},\\
    'outname'='${meta.id}',\\
    'log'='${meta.id}_collapse_command_log'))"

echo "${task.process}": > versions.yml
Rscript -e "cat(paste0('  enchantr: ',packageVersion('enchantr'),'\n'))" >> versions.yml

mv enchantr ${meta.id}_collapse_report
"""

NextFlow r-enchantr From line 22 of enchantr/collapse_duplicates.nf

"""
Rscript -e "enchantr::enchantr_report('define_clones', \\
                                    report_params=list('input'='${tabs.join(',')}', \\
                                    'imgt_db'='${imgt_base}', \\
                                    'cloneby'='${params.cloneby}', \\
                                    'force'=FALSE, \\
                                    'threshold'=${thr}, \\
                                    'singlecell'='${params.singlecell}','outdir'=getwd(), \\
                                    'nproc'=${task.cpus},\\
                                    'log'='${meta.id}_clone_command_log' ${args}))"

echo "${task.process}": > versions.yml
Rscript -e "cat(paste0('  enchantr: ',packageVersion('enchantr'),'\n'))" >> versions.yml

mv enchantr '${meta.id}_clone_report'
"""

NextFlow r-enchantr From line 44 of enchantr/define_clones.nf

"""
echo "${tabs.join('\n')}" > tabs.txt
Rscript -e "enchantr::enchantr_report('contamination', \\
    report_params=list('input'='tabs.txt',\\
    'input_id'='id','outdir'=getwd(), \\
    'outname'='cont-flag', \\
    'log'='all_reps_contamination_command_log'))"

echo "${task.process}": > versions.yml
Rscript -e "cat(paste0('  enchantr: ',packageVersion('enchantr'),'\n'))" >> versions.yml
mv enchantr all_reps_cont_report
"""

NextFlow r-enchantr From line 23 of enchantr/detect_contamination.nf

"""
Rscript -e "enchantr::enchantr_report('dowser_lineage', \\
                                    report_params=list('input'='${tabs}', \\
                                    'exec'='${params.igphyml}', \\
                                    'outdir'=getwd(), \\
                                    'nproc'=${task.cpus},\\
                                    'log'='${id_name}_dowser_command_log' ${args}))"

echo "${task.process}": > versions.yml
Rscript -e "cat(paste0('  enchantr: ',packageVersion('enchantr'),'\n'))" >> versions.yml

mv enchantr '${id_name}_dowser_report'
"""

NextFlow r-enchantr From line 41 of enchantr/dowser_lineages.nf

"""
Rscript -e "enchantr::enchantr_report('find_threshold', \\
    report_params=list('input'='${tab.join(',')}',\\
        'cloneby'='${params.cloneby}',\\
        'crossby'='${params.crossby}',\\
        'singlecell'='${params.singlecell}',\\
        'outdir'=getwd(),\\
        'nproc'=${task.cpus},\\
        'outname'='all_reps',\\
        'log'='all_reps_threshold_command_log',\\
        'logo'='${logo}' ${args}))"

echo "${task.process}": > versions.yml
Rscript -e "cat(paste0('  enchantr: ',packageVersion('enchantr'),'\n'))" >> versions.yml
mv enchantr all_reps_dist_report
"""

NextFlow r-enchantr From line 44 of enchantr/find_threshold.nf

"""
Rscript -e "enchantr:::enchantr_report('chimera_analysis', \\
    report_params=list('input'='${tab}',\\
    'outdir'=getwd(), \\
    'nproc'=${task.cpus},\\
    'outname'='${meta.id}', \\
    'log'='${meta.id}_chimeric_command_log'))"

echo "\"${task.process}\":" > versions.yml
Rscript -e "cat(paste0('  enchantr: ',packageVersion('enchantr'),'\n'))" >> versions.yml

mv enchantr ${meta.id}_chimera_report
"""

NextFlow r-enchantr From line 25 of enchantr/remove_chimeric.nf

"""
echo "${logs.join('\n')}" > logs.txt
Rscript -e "enchantr::enchantr_report('file_size', \\
    report_params=list('input'='logs.txt', 'metadata'='${metadata}',\\
    'outdir'=getwd()))"

echo "\"${task.process}\":" > versions.yml
Rscript -e "cat(paste0('  enchantr: ',packageVersion('enchantr'),'\n'))" >> versions.yml

mv enchantr file_size_report
"""

NextFlow r-enchantr From line 24 of enchantr/report_file_size.nf

"""
echo "${tabs.join('\n')}" > tabs.txt
Rscript -e "enchantr::enchantr_report('single_cell_qc', \\
    report_params=list('input'='tabs.txt',\\
    'outdir'=getwd(), \\
    'log'='all_reps_scqc_command_log'  ${args} ))"

echo "${task.process}": > versions.yml
Rscript -e "cat(paste0('  enchantr: ',packageVersion('enchantr'),'\n'))" >> versions.yml

mv enchantr all_reps_scqc_report
"""

NextFlow r-enchantr From line 39 of enchantr/single_cell_qc.nf

"""
Rscript -e "enchantr:::enchantr_report('validate_input', report_params=list('input'='${samplesheet}','collapseby'='${collapseby}','cloneby'='${cloneby}','reassign'='${params.reassign}','miairr'='${miairr}','outdir'=getwd()))"

echo "\"${task.process}\":" > versions.yml
Rscript -e "cat(paste0('  enchantr: ',packageVersion('enchantr'),'\n'))" >> versions.yml
"""

NextFlow r-enchantr From line 26 of enchantr/validate_input.nf

"""
[ ! -f  ${prefix}.fastq ] && ln -s $reads ${prefix}_ASSEMBLED.fastq
fastqc $args --threads $task.cpus ${prefix}_ASSEMBLED.fastq

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
END_VERSIONS
"""

NextFlow FastQC From line 22 of local/fastqc_postassembly.nf

"""
fetch_databases.sh

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    IMGT download date: \$( echo \$(date "+%F") )
    igblastn: \$( igblastn -version | grep -o "igblast[0-9\\. ]\\+" | grep -o "[0-9\\. ]\\+" )
    changeo: \$( AssignGenes.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow IgBLAST changeo From line 23 of local/fetch_databases.nf

"""
gunzip -f "${R1}"
gunzip -f "${R2}"

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
END_VERSIONS
"""

NextFlow From line 18 of local/gunzip.nf

"""
igblastn \
    -germline_db_V igblast_base/database/imgt_${meta.species}_${meta.locus.toLowerCase()}_v \
    -germline_db_D igblast_base/database/imgt_${meta.species}_${meta.locus.toLowerCase()}_d \
    -germline_db_J igblast_base/database/imgt_${meta.species}_${meta.locus.toLowerCase()}_j \
    -auxiliary_data igblast_base/optional_file/${meta.species}_gl.aux \
    -organism ${meta.species} \
    $args \
    -query $reads \
    -out ${meta.id}_db-pass.tsv

echo "START> AssignGenes" > ${meta.id}_changeo_assigngenes_command_log.txt
echo "COMMAND> igblast" >> ${meta.id}_changeo_assigngenes_command_log.txt
echo "VERSION> \$( igblastn -version | grep -o "igblast[0-9\\. ]\\+" | grep -o "[0-9\\. ]\\+" )" >> ${meta.id}_changeo_assigngenes_command_log.txt
echo "FILE> ${reads}" >> ${meta.id}_changeo_assigngenes_command_log.txt
echo "ORGANISM> ${meta.species}" >> ${meta.id}_changeo_assigngenes_command_log.txt
echo "LOCI> ${meta.locus.toLowerCase()}" >> ${meta.id}_changeo_assigngenes_command_log.txt
echo "NPROC> ${task.cpus}\n" >> ${meta.id}_changeo_assigngenes_command_log.txt
echo "PROGRESS> ...Done \n" >> ${meta.id}_changeo_assigngenes_command_log.txt
echo "PASS> \$(tail -n +2 ${meta.id}_db-pass.tsv | wc -l )" >> ${meta.id}_changeo_assigngenes_command_log.txt
echo "OUTPUT> ${meta.id}_igblast.fmt7" >> ${meta.id}_changeo_assigngenes_command_log.txt
echo "END> AssignGenes" >> ${meta.id}_changeo_assigngenes_command_log.txt

echo "START> MakeDB" > ${meta.id}_makedb_command_log.txt
echo "COMMAND> igblast" >> ${meta.id}_makedb_command_log.txt
echo "ALIGNER_FILE> ${meta.id}_igblast.fmt7" >> ${meta.id}_makedb_command_log.txt
echo "SEQ_FILE> ${reads}" >> ${meta.id}_makedb_command_log.txt
echo "ASIS_ID> False" >> ${meta.id}_makedb_command_log.txt
echo "ASIS_CALLS> False" >> ${meta.id}_makedb_command_log.txt
echo "VALIDATE> strict" >> ${meta.id}_makedb_command_log.txt
echo "EXTENDED> True" >> ${meta.id}_makedb_command_log.txt
echo "INFER_JUNCTION> False\n" >> ${meta.id}_makedb_command_log.txt
echo "PROGRESS> ...\n" >> ${meta.id}_makedb_command_log.txt
echo "PROGRESS> ... Done\n" >> ${meta.id}_makedb_command_log.txt
echo "OUTPUT> ${meta.id}_db-pass.tsv" >> ${meta.id}_makedb_command_log.txt
echo "PASS> \$(tail -n +2 ${meta.id}_db-pass.tsv | wc -l )" >> ${meta.id}_makedb_command_log.txt
echo "FAIL> 0" >> ${meta.id}_makedb_command_log.txt
echo "END> MakeDB" >> ${meta.id}_makedb_command_log.txt

echo "\"${task.process}\":" > versions.yml
echo "   igblastn: \$( igblastn -version | grep -o "igblast[0-9\\. ]\\+" | grep -o "[0-9\\. ]\\+" )" >> versions.yml
"""

NextFlow IgBLAST From line 23 of igblast/igblast_assigngenes.nf

"""
merge_R1_umi.py -R1 "${R1}" -I1 "${I1}" -o UMI_R1.fastq.gz --umi_start $params.umi_start --umi_length $params.umi_length
mv "UMI_R1.fastq.gz" "${meta.id}_UMI_R1.fastq.gz"
mv "${R2}" "${meta.id}_R2.fastq.gz"

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    python: \$( echo \$(python --version | grep -o "[0-9\\. ]\\+") )
    biopython: \$(echo \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('biopython').version)"))
END_VERSIONS
"""

NextFlow Biopython From line 19 of local/merge_UMI.nf

"""
log_parsing_no-umi.py

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    python: \$( echo \$(python --version | grep -o "[0-9\\. ]\\+") )
    pandas: \$(echo \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('pandas').version)"))
END_VERSIONS
"""

NextFlow Pandas From line 31 of local/parse_logs.nf

"""
log_parsing.py $clustersets

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    python: \$( echo \$(python --version | grep -o "[0-9\\. ]\\+") )
    pandas: \$(echo \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('pandas').version)"))
END_VERSIONS
"""

NextFlow Pandas From line 42 of local/parse_logs.nf

"""
AssemblePairs.py align -1 $R1 -2 $R2 --nproc ${task.cpus} \\
    $args \\
    --outname ${meta.id} --log ${meta.id}.log > ${meta.id}_command_log.txt
ParseLog.py -l ${meta.id}.log $args2

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( AssemblePairs.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 24 of presto/presto_assemblepairs.nf

"""
BuildConsensus.py -s $R1 --bf ${barcode_field} --nproc ${task.cpus} --pf PRIMER --prcons $params.primer_consensus --maxerror $params.buildconsensus_maxerror --maxgap $params.buildconsensus_maxgap --outname ${meta.id}_R1 --log ${meta.id}_R1.log > ${meta.id}_command_log.txt
BuildConsensus.py -s $R2 --bf ${barcode_field} --nproc ${task.cpus} --pf PRIMER --prcons $params.primer_consensus --maxerror $params.buildconsensus_maxerror --maxgap $params.buildconsensus_maxgap --outname ${meta.id}_R2 --log ${meta.id}_R2.log >> ${meta.id}_command_log.txt
ParseLog.py -l ${meta.id}_R1.log ${meta.id}_R2.log -f ID BARCODE SEQCOUNT PRIMER PRCOUNT PRCONS PRFREQ CONSCOUNT

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( BuildConsensus.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 24 of presto/presto_buildconsensus.nf

"""
ClusterSets.py set --nproc ${task.cpus} -s $R1 --outname ${meta.id}_R1 --exec vsearch --log ${meta.id}_R1.log > ${meta.id}_command_log.txt
ClusterSets.py set --nproc ${task.cpus} -s $R2 --outname ${meta.id}_R2 --exec vsearch --log ${meta.id}_R2.log >> ${meta.id}_command_log.txt
ParseLog.py -l ${meta.id}_R1.log ${meta.id}_R2.log -f ID BARCODE SEQCOUNT CLUSTERS

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( ClusterSets.py --version | awk -F' '  '{print \$2}' )
    vsearch: \$( vsearch --version &> vsearch.txt; cat vsearch.txt | head -n 1 | grep -o 'v[0-9\\.]\\+' )
END_VERSIONS
"""

NextFlow VSEARCH pRESTO From line 22 of presto/presto_clustersets.nf

"""
CollapseSeq.py -s $reads $args --outname ${meta.id} --log ${meta.id}.log > ${meta.id}_command_log.txt
ParseLog.py -l ${meta.id}.log $args2

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( CollapseSeq.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 26 of presto/presto_collapseseq.nf

"""
FilterSeq.py quality -s $R1 -q ${params.filterseq_q} --outname ${meta.id}_R1 --log ${R1.baseName}_R1.log --nproc ${task.cpus} > ${meta.id}_command_log.txt
FilterSeq.py quality -s $R2 -q ${params.filterseq_q} --outname ${meta.id}_R2 --log ${R2.baseName}_R2.log --nproc ${task.cpus} >> ${meta.id}_command_log.txt
ParseLog.py -l ${R1.baseName}_R1.log ${R2.baseName}_R2.log -f ID QUALITY

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( FilterSeq.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 23 of presto/presto_filterseq.nf

"""
FilterSeq.py quality -s $reads -q ${params.filterseq_q} --outname ${meta.id} --log ${reads.baseName}.log --nproc ${task.cpus} > ${meta.id}_command_log.txt
ParseLog.py -l ${reads.baseName}.log -f ID QUALITY

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( FilterSeq.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 22 of presto/presto_filterseq_postassembly.nf

"""
MaskPrimers.py score --nproc ${task.cpus} -s $R1 -p ${cprimers} $primer_start_R1 $revpr --maxerror ${params.primer_maxerror} --mode ${params.primer_mask_mode} --outname ${meta.id}_R1 --log ${meta.id}_R1.log > ${meta.id}_command_log.txt
MaskPrimers.py score --nproc ${task.cpus} -s $R2 -p ${vprimers} $primer_start_R2 $revpr --maxerror ${params.primer_maxerror} --mode ${params.primer_mask_mode} --outname ${meta.id}_R2 --log ${meta.id}_R2.log >> ${meta.id}_command_log.txt
ParseLog.py -l ${meta.id}_R1.log ${meta.id}_R2.log -f ID PRIMER ERROR

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( MaskPrimers.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 30 of presto/presto_maskprimers.nf

"""
MaskPrimers.py score --nproc ${task.cpus} -s $R1 -p ${vprimers} $primer_start_R1 $revpr --maxerror ${params.primer_maxerror} --mode ${params.primer_mask_mode} --outname ${meta.id}_R1 --log ${meta.id}_R1.log > ${meta.id}_command_log.txt
MaskPrimers.py score --nproc ${task.cpus} -s $R2 -p ${cprimers} $primer_start_R2 $revpr --maxerror ${params.primer_maxerror} --mode ${params.primer_mask_mode} --outname ${meta.id}_R2 --log ${meta.id}_R2.log >> ${meta.id}_command_log.txt
ParseLog.py -l "${meta.id}_R1.log" "${meta.id}_R2.log" -f ID PRIMER ERROR

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( MaskPrimers.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 43 of presto/presto_maskprimers.nf

"""
MaskPrimers.py score --nproc ${task.cpus} -s $reads -p ${cprimers} --start ${params.cprimer_start} --maxerror ${params.primer_maxerror} \
    --mode ${params.primer_mask_mode} --outname ${meta.id}-FWD \
    --log ${meta.id}-FWD.log > ${meta.id}_command_log.txt
MaskPrimers.py score --nproc ${task.cpus} -s ${meta.id}-FWD_primers-pass.fastq -p ${vprimers} --start ${params.vprimer_start} --maxerror ${params.primer_maxerror} \
    --mode ${params.primer_mask_mode} --outname ${meta.id}-REV $revpr \
    --log ${meta.id}-REV.log >> ${meta.id}_command_log.txt
ParseLog.py -l ${meta.id}-FWD.log ${meta.id}-REV.log -f ID PRIMER ERROR

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( MaskPrimers.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 26 of presto/presto_maskprimers_postassembly.nf

"""
MaskPrimers.py score --nproc ${task.cpus} -s $reads -p ${vprimers} --start ${params.cprimer_start} --maxerror ${params.primer_maxerror} \
    --mode ${params.primer_mask_mode} --outname ${meta.id}-FWD \
    --log ${meta.id}-FWD.log > ${meta.id}_command_log.txt
MaskPrimers.py score --nproc ${task.cpus} -s ${meta.id}-FWD_primers-pass.fastq -p ${cprimers} --start ${params.vprimer_start} --maxerror ${params.primer_maxerror} \
    --mode ${params.primer_mask_mode} --outname ${meta.id}-REV $revpr \
    --log ${meta.id}-REV.log >> ${meta.id}_command_log.txt
ParseLog.py -l ${meta.id}-FWD.log ${meta.id}-REV.log -f ID PRIMER ERROR

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( MaskPrimers.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 41 of presto/presto_maskprimers_postassembly.nf

"""
PairSeq.py -1 ${meta.id}_R1.fastq -2 ${meta.id}_R2.fastq $copyfield --coord illumina > ${meta.id}_command_log.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( PairSeq.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 21 of presto/presto_pairseq.nf

"""
ParseHeaders.py copy -s $R1 -f BARCODE -k CLUSTER --act cat > ${meta.id}_command_log.txt
ParseHeaders.py copy -s $R2 -f BARCODE -k CLUSTER --act cat >> ${meta.id}_command_log.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( ParseHeaders.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 21 of presto/presto_parse_cluster.nf

"""
ParseHeaders.py add -s $reads -o ${reads.baseName}_reheader-pass.fastq $args -u ${meta.id} ${meta.subject_id} ${meta.species} ${meta.locus}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( ParseHeaders.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 20 of presto/presto_parseheaders_metadata.nf

"""
ParseHeaders.py $subcommand -s $reads -o ${reads.baseName}_reheader-pass.fastq $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( ParseHeaders.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 21 of presto/presto_parseheaders.nf

"""
ParseHeaders.py copy -s $reads -o ${reads.baseName}_reheader-pass.fastq -f $args --act first last -k C_PRIMER V_PRIMER

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( ParseHeaders.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 21 of presto/presto_parseheaders_primers.nf

"""
ParseHeaders.py copy -s $reads -o ${reads.baseName}_reheader-pass.fastq -f $args --act first last -k V_PRIMER C_PRIMER

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( ParseHeaders.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 30 of presto/presto_parseheaders_primers.nf

"""
PairSeq.py -1 ${meta.id}_R1.fastq -2 ${meta.id}_R2.fastq --coord presto > ${meta.id}_command_log.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( PairSeq.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 20 of presto/presto_postconsensus_pairseq.nf

"""
SplitSeq.py group -s $reads \\
$args \\
--outname ${meta.id} \\
--fasta > ${meta.id}_command_log.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    presto: \$( SplitSeq.py --version | awk -F' '  '{print \$2}' )
END_VERSIONS
"""

NextFlow pRESTO From line 21 of presto/presto_splitseq.nf

"""
mv "${R1}" "${meta.id}_R1.fastq.gz"
mv "${R2}" "${meta.id}_R2.fastq.gz"
"""

NextFlow From line 18 of local/rename_fastq.nf

"""
reveal_add_metadata.R --repertoire ${tab} --metadata ${validated_input} --input_id ${meta.id} --outname ${meta.id} > ${meta.id}_add-meta_command_log.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    dplyr: \$(Rscript -e "library(dplyr); cat(paste(packageVersion('dplyr'), collapse='.'))")
    optparse: \$(Rscript -e "library(optparse); cat(paste(packageVersion('optparse'), collapse='.'))")
    R: \$(echo \$(R --version 2>&1) | awk -F' '  '{print \$3}')
END_VERSIONS
"""

NextFlow From line 23 of reveal/add_meta_to_tab.nf

"""
reveal_mod_3_junction.R --repertoire $tab --outname ${meta.id} > ${meta.id}_jmod3_command_log.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    alakazam: \$(Rscript -e "library(alakazam); cat(paste(packageVersion('alakazam'), collapse='.'))")
    optparse: \$(Rscript -e "library(optparse); cat(paste(packageVersion('optparse'), collapse='.'))")
    airr: \$(Rscript -e "library(airr); cat(paste(packageVersion('airr'), collapse='.'))")
    R: \$(echo \$(R --version 2>&1) | awk -F' '  '{print \$3}')
END_VERSIONS
"""

NextFlow airr From line 20 of reveal/filter_junction_mod3.nf

"""
reveal_filter_quality.R --repertoire $tab --outname ${meta.id} > ${meta.id}_fq_command_log.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    alakazam: \$(Rscript -e "library(alakazam); cat(paste(packageVersion('alakazam'), collapse='.'))")
    optparse: \$(Rscript -e "library(optparse); cat(paste(packageVersion('optparse'), collapse='.'))")
    stringi: \$(Rscript -e "library(stringi); cat(paste(packageVersion('stringi'), collapse='.'))")
    dplyr: \$(Rscript -e "library(dplyr); cat(paste(packageVersion('dplyr'), collapse='.'))")
    airr: \$(Rscript -e "library(airr); cat(paste(packageVersion('airr'), collapse='.'))")
    DT: \$(Rscript -e "library(DT); cat(paste(packageVersion('DT'), collapse='.'))")
    R: \$(echo \$(R --version 2>&1) | awk -F' '  '{print \$3}')
END_VERSIONS
"""

NextFlow airr From line 20 of reveal/filter_quality.nf

"""
check_samplesheet.py $samplesheet
cp $samplesheet samplesheet.valid.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    python: \$( echo \$(python --version | grep -o "[0-9\\. ]\\+") )
    pandas: \$(echo \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('pandas').version)"))
END_VERSIONS
"""

NextFlow Pandas From line 21 of local/samplesheet_check.nf

"""
unzip $archive

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    unzip: \$(echo \$(unzip -help 2>&1) | sed 's/^.*UnZip //; s/ of.*\$//')
END_VERSIONS
"""

NextFlow From line 19 of local/unzip_db.nf

"""
[ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz

fastp \\
    --stdout \\
    --in1 ${prefix}.fastq.gz \\
    --thread $task.cpus \\
    --json ${prefix}.fastp.json \\
    --html ${prefix}.fastp.html \\
    $adapter_list \\
    $fail_fastq \\
    $args \\
    2> ${prefix}.fastp.log \\
| gzip -c > ${prefix}.fastp.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
END_VERSIONS
"""

NextFlow fastp From line 36 of fastp/main.nf

"""
[ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz

fastp \\
    --in1 ${prefix}.fastq.gz \\
    --out1  ${prefix}.fastp.fastq.gz \\
    --thread $task.cpus \\
    --json ${prefix}.fastp.json \\
    --html ${prefix}.fastp.html \\
    $adapter_list \\
    $fail_fastq \\
    $args \\
    2> ${prefix}.fastp.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
END_VERSIONS
"""

NextFlow fastp From line 57 of fastp/main.nf

"""
[ ! -f  ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz
[ ! -f  ${prefix}_2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_2.fastq.gz
fastp \\
    --in1 ${prefix}_1.fastq.gz \\
    --in2 ${prefix}_2.fastq.gz \\
    --out1 ${prefix}_1.fastp.fastq.gz \\
    --out2 ${prefix}_2.fastp.fastq.gz \\
    --json ${prefix}.fastp.json \\
    --html ${prefix}.fastp.html \\
    $adapter_list \\
    $fail_fastq \\
    $merge_fastq \\
    --thread $task.cpus \\
    --detect_adapter_for_pe \\
    $args \\
    2> ${prefix}.fastp.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
END_VERSIONS
"""

NextFlow fastp From line 78 of fastp/main.nf

"""
[ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
fastqc $args --threads $task.cpus ${prefix}.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
END_VERSIONS
"""

NextFlow FastQC From line 26 of fastqc/main.nf

"""
[ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
[ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
END_VERSIONS
"""

NextFlow FastQC From line 36 of fastqc/main.nf

"""
touch ${prefix}.html
touch ${prefix}.zip

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
END_VERSIONS
"""

NextFlow FastQC From line 50 of fastqc/main.nf

"""
multiqc \\
    --force \\
    $args \\
    $config \\
    $extra_config \\
    .

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS
"""

NextFlow MultiQC From line 28 of multiqc/main.nf

"""
touch multiqc_data
touch multiqc_plots
touch multiqc_report.html

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS
"""