diff --git a/README.md b/README.md index bb7050b..ca771c1 100644 --- a/README.md +++ b/README.md @@ -23,10 +23,11 @@ Command-line interface (CLI) for running bioinformatics workflows written in nex Download the latest stable release [here](https://github.com/pirl-unc/nexus/releases) +Make sure to have `nextflow v24.10.0` and up: ``` conda create -n nexus python=3.10 conda activate nexus -conda install bioconda::nextflow==23.10.0 +conda install bioconda::nextflow==24.10.0 pip install nexus-.tar.gz --verbose ``` diff --git a/src/nexuslib/pipelines/quantification/long_read_rna_quantification_oarfish/README.md b/src/nexuslib/pipelines/quantification/long_read_rna_quantification_oarfish/README.md index 3d34f5b..0dc13f1 100644 --- a/src/nexuslib/pipelines/quantification/long_read_rna_quantification_oarfish/README.md +++ b/src/nexuslib/pipelines/quantification/long_read_rna_quantification_oarfish/README.md @@ -22,7 +22,7 @@ nexus run --nf-workflow long_read_rna_quantification_oarfish.nf \ --samples_tsv_file SAMPLES_TSV_FILE \ --reference_transcriptome_fasta_file REFERENCE_TRANSCRIPTOME_FASTA_FILE \ --output_dir OUTPUT_DIR \ - --params_oarfish '"--seq-tech pac-bio-hifi"' + --params_oarfish '"--seq-tech pac-bio-hifi "' ``` ### Usage @@ -40,7 +40,7 @@ required arguments: 'sample_id', 'fastq_file'. --reference_transcriptome_fasta_file : Reference transcriptome FASTA file (default: '/datastore/lbcfs/collaborations/pirl/seqdata/references/gencode.v41.transcripts.fa'). - --params_oarfish : Oarfish parameters (default: '"--seq-tech pac-bio-hifi"'). + --params_oarfish : Oarfish parameters (default: '"--seq-tech pac-bio-hifi "'). Note that the parameters need to be wrapped in quotes and a space at the end of the string is necessary. --output_dir : Directory to which output files will be copied. diff --git a/src/nexuslib/pipelines/quantification/long_read_rna_quantification_oarfish/long_read_rna_quantification_oarfish.nf b/src/nexuslib/pipelines/quantification/long_read_rna_quantification_oarfish/long_read_rna_quantification_oarfish.nf index ed42db8..b38eee5 100644 --- a/src/nexuslib/pipelines/quantification/long_read_rna_quantification_oarfish/long_read_rna_quantification_oarfish.nf +++ b/src/nexuslib/pipelines/quantification/long_read_rna_quantification_oarfish/long_read_rna_quantification_oarfish.nf @@ -46,7 +46,7 @@ if (params.help) { 'sample_id', 'fastq_file'. --reference_transcriptome_fasta_file : Reference transcriptome FASTA file (default: '/datastore/lbcfs/collaborations/pirl/seqdata/references/gencode.v41.transcripts.fa'). - --params_oarfish : Oarfish parameters (default: '"--seq-tech pac-bio-hifi"'). + --params_oarfish : Oarfish parameters (default: '"--seq-tech pac-bio-hifi "'). Note that the parameters need to be wrapped in quotes and a space at the end of the string is necessary. --output_dir : Directory to which output files will be copied. diff --git a/test/quantification/test_long_read_rna_quantification_oarfish.py b/test/quantification/test_long_read_rna_quantification_oarfish.py index 5b06c65..980574c 100644 --- a/test/quantification/test_long_read_rna_quantification_oarfish.py +++ b/test/quantification/test_long_read_rna_quantification_oarfish.py @@ -28,7 +28,7 @@ def test_long_read_rna_quantification_oarfish(): '-w', work_dir, '--samples_tsv_file', intermediate_dir + '/samples.tsv', '--reference_transcriptome_fasta_file', reference_transcriptome_fasta_file, - '--params_oarfish', '"--seq-tech pac-bio-hifi"', + '--params_oarfish', '"--seq-tech pac-bio-hifi "', '--output_dir', output_dir ] run_workflow(workflow='long_read_rna_quantification_oarfish.nf',