From 2e0eb69b953d5748fe5faad78f13ea95698a37b9 Mon Sep 17 00:00:00 2001 From: subwaystation Date: Thu, 26 Nov 2020 14:21:06 +0100 Subject: [PATCH 1/5] fix pggb docker image to 20201125163549e465b0 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index e17cd5a0..b67da204 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/pangenome/pggb:latest +FROM ghcr.io/pangenome/pggb:20201125163549e465b0 LABEL authors="Simon Heumos, Michael Heuer, Lukas Heumos, Erik Garrison, Andrea Guarracino" \ description="Docker image containing all software requirements for the nf-core/pangenome pipeline" From 2cae5451f422b4a6a468dc65f8069dd8a254abe2 Mon Sep 17 00:00:00 2001 From: Zethson Date: Sun, 29 Nov 2020 17:02:55 +0100 Subject: [PATCH 2/5] extracted parameters from main.nf into nextflow.config Signed-off-by: Zethson --- main.nf | 17 ----------------- nextflow.config | 18 ++++++++++++++++-- 2 files changed, 16 insertions(+), 19 deletions(-) diff --git a/main.nf b/main.nf index bfed9710..bc2ac4fc 100644 --- a/main.nf +++ b/main.nf @@ -11,23 +11,6 @@ nextflow.enable.dsl = 2 -params.input="${baseDir}/**.fa.gz" -params.map_pct_id=90//false -params.align_pct_id=90// false -params.n_secondary=10//false -params.segment_length=1000//false -params.mash_kmer=16 -params.min_match_length=8 -params.max_block_weight=10000 -params.max_path_jump=5000 -params.min_subpath=0 -params.max_edge_jump=5000 -params.max_poa_length=10000 -params.do_viz=false -params.do_layout=false -params.do_stats=false -params.consensus_jump_max="10,100,1000,10000" - def makeBaseName = { f -> """\ ${f.getSimpleName()}.pggb-\ s${params.segment_length}-\ diff --git a/nextflow.config b/nextflow.config index ab37384d..a9b75685 100644 --- a/nextflow.config +++ b/nextflow.config @@ -9,9 +9,23 @@ params { // Workflow flags - // TODO nf-core: Specify your pipeline's command line flags + input="${baseDir}/**.fa.gz" + map_pct_id=90//false + align_pct_id=90// false + n_secondary=10//false + segment_length=1000//false + mash_kmer=16 + min_match_length=8 + max_block_weight=10000 + max_path_jump=5000 + min_subpath=0 + max_edge_jump=5000 + max_poa_length=10000 + do_viz=false + do_layout=false + do_stats=false + consensus_jump_max="10,100,1000,10000" genome = false - input = "data/*.fa.gz" outdir = './results' publish_dir_mode = 'copy' From 082540100b49796bb1218817eb859d3e65435df7 Mon Sep 17 00:00:00 2001 From: subwaystation Date: Mon, 30 Nov 2020 15:18:22 +0100 Subject: [PATCH 3/5] add module name prefix to parameters --- main.nf | 42 +++++++++++++++++++++--------------------- nextflow.config | 48 +++++++++++++++++++++++++++++++----------------- 2 files changed, 52 insertions(+), 38 deletions(-) diff --git a/main.nf b/main.nf index bc2ac4fc..d3f334ba 100644 --- a/main.nf +++ b/main.nf @@ -13,16 +13,16 @@ nextflow.enable.dsl = 2 def makeBaseName = { f -> """\ ${f.getSimpleName()}.pggb-\ -s${params.segment_length}-\ -p${params.map_pct_id}-\ -n${params.n_secondary}-\ -a${params.align_pct_id}-\ -K${params.mash_kmer}-\ -k${params.min_match_length}-\ -w${params.max_block_weight}-\ -j${params.max_path_jump}-\ -W${params.min_subpath}-\ -e${params.max_edge_jump}\ +s${params.edyeet_segment_length}-\ +p${params.edyeet_map_pct_id}-\ +n${params.edyeet_n_secondary}-\ +a${params.edyeet_align_pct_id}-\ +K${params.edyeet_mash_kmer}-\ +k${params.seqwish_min_match_length}-\ +w${params.smoothxg_max_block_weight}-\ +j${params.smoothxg_max_path_jump}-\ +W${params.smoothxg_min_subpath}-\ +e${params.smoothxg_max_edge_jump}\ """ } fasta = channel.fromPath("${params.input}").map { f -> tuple(makeBaseName(f), f) } @@ -36,11 +36,11 @@ process edyeet { """ edyeet -X \ - -s ${params.segment_length} \ - -p ${params.map_pct_id} \ - -n ${params.n_secondary} \ - -a ${params.align_pct_id} \ - -k ${params.mash_kmer} \ + -s ${params.edyeet_segment_length} \ + -p ${params.edyeet_map_pct_id} \ + -n ${params.edyeet_n_secondary} \ + -a ${params.edyeet_align_pct_id} \ + -k ${params.edyeet_mash_kmer} \ -t ${task.cpus} \ $fasta $fasta \ >${f}.paf @@ -61,7 +61,7 @@ process seqwish { -t ${task.cpus} \ -s $fasta \ -p $alignment \ - -k ${params.min_match_length} \ + -k ${params.seqwish_min_match_length} \ -g ${f}.seqwish.gfa -P """ } @@ -80,15 +80,15 @@ process smoothxg { smoothxg \ -t ${task.cpus} \ -g $graph \ - -w ${params.max_block_weight} \ - -j ${params.max_path_jump} \ - -e ${params.max_edge_jump} \ - -l ${params.max_poa_length} \ + -w ${params.smoothxg_max_block_weight} \ + -j ${params.smoothxg_max_path_jump} \ + -e ${params.smoothxg_max_edge_jump} \ + -l ${params.smoothxg_max_poa_length} \ -o ${f}.smooth.gfa \ -m ${f}.smooth.maf \ -s ${f}.consensus \ -a \ - -C ${params.consensus_jump_max} + -C ${params.smoothxg_consensus_jump_max} """ } diff --git a/nextflow.config b/nextflow.config index a9b75685..c98ea7e6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -8,28 +8,40 @@ // Global default params, used in configs params { - // Workflow flags + // Input options input="${baseDir}/**.fa.gz" - map_pct_id=90//false - align_pct_id=90// false - n_secondary=10//false - segment_length=1000//false - mash_kmer=16 - min_match_length=8 - max_block_weight=10000 - max_path_jump=5000 - min_subpath=0 - max_edge_jump=5000 - max_poa_length=10000 - do_viz=false - do_layout=false - do_stats=false - consensus_jump_max="10,100,1000,10000" - genome = false + + // Reporting + do_stats=true + + // Edyeet options + edyeet_map_pct_id=90 + edyeet_align_pct_id=90 + edyeet_n_secondary=10 + edyeet_segment_length=1000 + edyeet_mash_kmer=16 + + // Seqwish options + seqwish_min_match_length=8 + + // Smoothxg options + smoothxg_max_block_weight=10000 + smoothxg_max_path_jump=5000 + smoothxg_min_subpath=0 + smoothxg_max_edge_jump=5000 + smoothxg_max_poa_length=10000 + smoothxg_consensus_jump_max="10,100,1000,10000" + + // Visualization + do_viz = false + do_layout = false + + // Output options outdir = './results' publish_dir_mode = 'copy' // Boilerplate options + genome = '' name = false multiqc_config = false email = false @@ -41,6 +53,8 @@ params { igenomes_base = 's3://ngi-igenomes/igenomes/' tracedir = "${params.outdir}/pipeline_info" igenomes_ignore = false + + // Config options custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" hostnames = false From 5af6fc12a144c4bc6c0104e9e2f40d504e1e6c15 Mon Sep 17 00:00:00 2001 From: subwaystation Date: Mon, 30 Nov 2020 15:24:48 +0100 Subject: [PATCH 4/5] set nextflow.config.manifest.nextflowVersion to >=20.10.0 --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index c98ea7e6..6a03b5fe 100644 --- a/nextflow.config +++ b/nextflow.config @@ -143,7 +143,7 @@ manifest { homePage = 'https://github.com/nf-core/pangenome' description = 'The pangenome graph construction pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs' mainScript = 'main.nf' - nextflowVersion = '>=20.04.0' + nextflowVersion = '>=20.10.0' version = '1.0dev' } From b8afe1c9aa8e3cf0adea4ed868d1f04907fae47b Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Mon, 30 Nov 2020 15:56:03 +0100 Subject: [PATCH 5/5] Fixed minimum NF badge in Readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8d9bf181..349357b8 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ [![GitHub Actions CI Status](https://github.com/nf-core/pangenome/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/pangenome/actions) [![GitHub Actions Linting Status](https://github.com/nf-core/pangenome/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/pangenome/actions) -[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.04.0-brightgreen.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.10.0-brightgreen.svg)](https://www.nextflow.io/) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/) [![Docker](https://img.shields.io/docker/automated/nfcore/pangenome.svg)](https://hub.docker.com/r/nfcore/pangenome)