update docs

pirl-unc · Nov 4, 2024 · ad4cdae · ad4cdae
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Showing 4 changed files with 6 additions and 5 deletions.
diff --git 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-<version>.tar.gz --verbose
 ```
 

diff --git a/...exuslib/pipelines/quantification/long_read_rna_quantification_oarfish/README.md b/...exuslib/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/...antification/long_read_rna_quantification_oarfish/long_read_rna_quantification_oarfish.nf b/...antification/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
@@ -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',