From 242fdb2f73179ab220540c95343d8ba2a60b5a87 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 6 Apr 2021 13:38:41 +0100 Subject: [PATCH] Version bumps and minor module updates (#406) * Version bumps and minor module updates * Fix Pangolin tests * Fix SPAdes tests * stageAs @phue --- software/pangolin/main.nf | 6 ++--- software/rsem/preparereference/main.nf | 9 ++++--- software/spades/main.nf | 10 ++++---- software/spades/meta.yml | 5 ---- tests/software/pangolin/test.yml | 2 +- tests/software/spades/main.nf | 27 ++------------------- tests/software/spades/test.yml | 33 ++------------------------ 7 files changed, 16 insertions(+), 76 deletions(-) diff --git a/software/pangolin/main.nf b/software/pangolin/main.nf index 10127052..dfc06ef3 100644 --- a/software/pangolin/main.nf +++ b/software/pangolin/main.nf @@ -11,11 +11,11 @@ process PANGOLIN { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? 'bioconda::pangolin=2.3.2' : null) + conda (params.enable_conda ? 'bioconda::pangolin=2.3.8' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container 'https://depot.galaxyproject.org/singularity/pangolin:2.3.2--py_0' + container 'https://depot.galaxyproject.org/singularity/pangolin:2.3.8--py_0' } else { - container 'quay.io/biocontainers/pangolin:2.3.2--py_0' + container 'quay.io/biocontainers/pangolin:2.3.8--py_0' } input: diff --git a/software/rsem/preparereference/main.nf b/software/rsem/preparereference/main.nf index 633b3d90..6d76515f 100644 --- a/software/rsem/preparereference/main.nf +++ b/software/rsem/preparereference/main.nf @@ -19,12 +19,13 @@ process RSEM_PREPAREREFERENCE { } input: - path fasta + path fasta, stageAs: "rsem/*" path gtf output: - path "rsem" , emit: index - path "*.version.txt", emit: version + path "rsem" , emit: index + path "rsem/*transcripts.fa", emit: transcript_fasta + path "*.version.txt" , emit: version script: def software = getSoftwareName(task.process) @@ -33,7 +34,6 @@ process RSEM_PREPAREREFERENCE { args.removeIf { it.contains('--star') } def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : '' """ - mkdir rsem STAR \\ --runMode genomeGenerate \\ --genomeDir rsem/ \\ @@ -54,7 +54,6 @@ process RSEM_PREPAREREFERENCE { """ } else { """ - mkdir rsem rsem-prepare-reference \\ --gtf $gtf \\ --num-threads $task.cpus \\ diff --git a/software/spades/main.nf b/software/spades/main.nf index badceb76..c9e1e142 100644 --- a/software/spades/main.nf +++ b/software/spades/main.nf @@ -11,17 +11,16 @@ process SPADES { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::spades=3.15.0" : null) + conda (params.enable_conda ? "bioconda::spades=3.15.2" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/spades:3.15.0--h633aebb_0" + container "https://depot.galaxyproject.org/singularity/spades:3.15.2--h95f258a_1" } else { - container "quay.io/biocontainers/spades:3.15.0--h633aebb_0" + container "quay.io/biocontainers/spades:3.15.2--h95f258a_1" } input: tuple val(meta), path(reads) path hmm - val coronaspades output: tuple val(meta), path('*.scaffolds.fa') , optional:true, emit: scaffolds @@ -37,9 +36,8 @@ process SPADES { def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def input_reads = meta.single_end ? "-s $reads" : "-1 ${reads[0]} -2 ${reads[1]}" def custom_hmms = params.spades_hmm ? "--custom-hmms $hmm" : "" - def command = coronaspades ? "coronaspades.py" : "spades.py" """ - $command \\ + spades.py \\ $options.args \\ --threads $task.cpus \\ $custom_hmms \\ diff --git a/software/spades/meta.yml b/software/spades/meta.yml index d1ea7de3..5a05e5f3 100644 --- a/software/spades/meta.yml +++ b/software/spades/meta.yml @@ -29,11 +29,6 @@ input: type: file description: File or directory with amino acid HMMs for Spades HMM-guided mode. - - coronaspades: - type: boolean - description: | - Run coronaspades instead of default spades mode. coronaSPAdes is a special - mode of rnaviralSPAdes specifically aimed for SARS-CoV-2 de novo assembly. output: - meta: type: map diff --git a/tests/software/pangolin/test.yml b/tests/software/pangolin/test.yml index 494c057e..ea7a0b71 100644 --- a/tests/software/pangolin/test.yml +++ b/tests/software/pangolin/test.yml @@ -4,4 +4,4 @@ - pangolin files: - path: ./output/pangolin/test.pangolin.csv - md5sum: 1d513775cec0901ebee1359c91035d3a + md5sum: c8b1720f98c9e032908f61bbc05a0fe2 diff --git a/tests/software/spades/main.nf b/tests/software/spades/main.nf index 150d1569..41fbe673 100644 --- a/tests/software/spades/main.nf +++ b/tests/software/spades/main.nf @@ -8,9 +8,7 @@ workflow test_spades_single_end { input = [ [ id:'test', single_end:true ], // meta map [ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ] - coronaspades = false - - SPADES ( input, [], coronaspades ) + SPADES ( input, [] ) } workflow test_spades_paired_end { @@ -18,27 +16,6 @@ workflow test_spades_paired_end { [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ] - coronaspades = false - SPADES ( input, [], coronaspades ) + SPADES ( input, [] ) } - -workflow test_coronospades_single_end { - input = [ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] - ] - coronaspades = true - - SPADES ( input, [], coronaspades ) -} - -workflow test_coronospades_paired_end { - input = [ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] - ] - coronaspades = true - - SPADES ( input, [], coronaspades ) -} - diff --git a/tests/software/spades/test.yml b/tests/software/spades/test.yml index bf24fab2..5b6c800a 100644 --- a/tests/software/spades/test.yml +++ b/tests/software/spades/test.yml @@ -19,36 +19,7 @@ - spades_paired_end files: - path: output/spades/test.assembly.gfa - md5sum: d546f9042f5ff911757e895e7b21f620 + md5sum: faf76135ee390606b899c0197dc38e04 - path: output/spades/test.contigs.fa - md5sum: f3e87d68521aa485d70aecd82de519b4 + md5sum: 6148e25b33890c80f176f90f2dd88989 - path: output/spades/test.spades.log - -- name: coronaspades single end - command: nextflow run ./tests/software/spades -entry test_coronospades_single_end -c tests/config/nextflow.config - tags: - - spades - - coronaspades_single_end - files: - - path: output/spades/test.assembly.gfa - md5sum: 46531ec9b845c1a1cb469627688fecb7 - - path: output/spades/test.contigs.fa - md5sum: f2c4a48ebba560aa5c8fde04dbe905fc - - path: output/spades/test.scaffolds.fa - md5sum: f2c4a48ebba560aa5c8fde04dbe905fc - - path: output/spades/test.gene_clusters.fa - - path: output/spades/test.spades.log - -- name: coronaspades paired end - command: nextflow run ./tests/software/spades -entry test_coronospades_paired_end -c tests/config/nextflow.config - tags: - - spades - - coronaspades_paired_end - files: - - path: output/spades/test.assembly.gfa - md5sum: d546f9042f5ff911757e895e7b21f620 - - path: output/spades/test.contigs.fa - md5sum: f3e87d68521aa485d70aecd82de519b4 - - path: output/spades/test.gene_clusters.fa - - path: output/spades/test.spades.log -