From 72fe4fffe69450471d03233224646ef8b230a4c3 Mon Sep 17 00:00:00 2001 From: James Zlosnik <38386229+JamesZlosnik@users.noreply.github.com> Date: Tue, 17 Dec 2024 15:44:46 -0800 Subject: [PATCH] 14 remove defaults channel (#15) * remove default channel * fix typo * update dehosting conda env * fix name of dehosting_index param in docs * bump version --------- Co-authored-by: Dan Fornika --- README.md | 8 ++++---- environments/dehosting.yml | 1 - environments/environment.yml | 1 - nextflow.config | 2 +- 4 files changed, 5 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 71ae2a9..29aa2a1 100644 --- a/README.md +++ b/README.md @@ -57,7 +57,7 @@ that align with sufficient quality and specificity. 1. Activate the conda environment that is used by this pipeline for dehosting. ``` -conda activate basic-sequence-qc-dehosting-6e4260b30b21d1dbd469b1b1e0f20628 +conda activate basic-sequence-qc-dehosting-eeb6f6f753e1d37317d1d06b4e3141d5 ``` 2. Download (fetch) the default reference genome (`human-t2t-hla`) @@ -111,7 +111,7 @@ nextflow run BCCDC-PHL/basic-sequence-qc \ --cache ~/.conda/envs \ --fastq_input /path/to/fastq_input \ --dehost \ - --outidr /path/to/output-dir + --outdir /path/to/output-dir ``` By default, the `human-t2t-hla` reference will be used. To use an alternative reference, include the `--dehosting_index` flag along @@ -123,8 +123,8 @@ nextflow run BCCDC-PHL/basic-sequence-qc \ --cache ~/.conda/envs \ --fastq_input /path/to/fastq_input \ --dehost \ - --dehosting_reference human-t2t-hla-argos985-mycob140 \ - --outidr /path/to/output-dir + --dehosting_index human-t2t-hla-argos985-mycob140 \ + --outdir /path/to/output-dir ``` ## Output diff --git a/environments/dehosting.yml b/environments/dehosting.yml index ee6437e..2b6572c 100644 --- a/environments/dehosting.yml +++ b/environments/dehosting.yml @@ -2,7 +2,6 @@ name: basic-sequence-qc-dehosting channels: - conda-forge - bioconda - - defaults dependencies: - python=3 - hostile=1.1.0 diff --git a/environments/environment.yml b/environments/environment.yml index 531e86d..441d8bc 100644 --- a/environments/environment.yml +++ b/environments/environment.yml @@ -2,7 +2,6 @@ name: basic-sequence-qc channels: - conda-forge - bioconda - - defaults dependencies: - python=3 - fastp=0.23.4 diff --git a/nextflow.config b/nextflow.config index 77b7149..58bc9e6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -3,7 +3,7 @@ manifest { description = 'Basic Sequence QC' mainScript = 'main.nf' nextflowVersion = '>=20.01.0' - version = '0.3.0' + version = '0.3.1' }