The source code should never be modified when running our pipelines
Create a config file for input, output, and parameters. An example for a config file can be found here. See Inputs for the detailed description of each variable in the config file. The config file can be generated using a python script (see below).
+Create a config file for input, output, and parameters. An example for a config file can be found here. See Inputs for the detailed description of each variable in the config file. The config file can be generated using a python script (see below).
Do not directly modify the source template.config, but rather you should copy it from the pipeline release folder to your project-specific folder and modify it there
Create the input csv using the template. The example csv is a single-lane sample, however this pipeline can take multi-lane sample as well, with each record in the csv file representing a lane (a pair of fastq). All records must have the same value in the sample column. See Inputs for detailed description of each column. All columns must exist in order to run the pipeline successfully.
+Create the input csv using the template. The example csv is a single-lane sample, however this pipeline can take multi-lane sample as well, with each record in the csv file representing a lane (a pair of fastq). All records must have the same value in the sample column. See Inputs for detailed description of each column. All columns must exist in order to run the pipeline successfully.
Again, do not directly modify the source template csv file. Instead, copy it from the pipeline release folder to your project-specific folder and modify it there.
@@ -145,7 +145,7 @@path/to/main.nf could be: /hot/software/pipeline/pipeline-align-DNA/Nextflow/release/8.0.0/pipeline/align-DNA.nfpath/to/sample-specific.config is the path to where you saved your project-specific copy of template.configpath/to/sample-specific.config is the path to where you saved your project-specific copy of template.configTo submit to UCLAHS-CDS's Azure cloud, use the submission script here with the command below:
python path/to/submit_nextflow_pipeline.py \
@@ -156,7 +156,7 @@ How To Run
--email jdoe@ucla.edu
BWA-MEM2 Genome Index
-The reference genome index must be generated by BWA-MEM2 with the correct version. Genome index generated by old BWA-MEM2 versions or the original BWA is not accepted. The reference genome index can be generated using the generate-genome-index.nf nextflow pipeline. To run this pipeline, you need to create a config file using this template to specify the path of reference_fasta and the temp_dir. The temp_dir is used to store intermediate files of Nextflow. The genome index files are saved to the same directory of the input reference FASTA by the pipeline. Use the command below to run this generate genome index pipeline:
generate-genome-index.nf nextflow pipeline. To run this pipeline, you need to create a config file using this template to specify the path of reference_fasta and the temp_dir. The temp_dir is used to store intermediate files of Nextflow. The genome index files are saved to the same directory of the input reference FASTA by the pipeline. Use the command below to run this generate genome index pipeline:
nextflow run path/to/generate-genome-index.nf -config path/to/genome-specific.config
This can also be submitted using the submission script to the UCLAHS-CDS's Azure cloud as mentioned above.
diff --git a/development/index.html b/development/index.html index 8593aef..fdf0b44 100644 --- a/development/index.html +++ b/development/index.html @@ -102,7 +102,7 @@-The input csv must have all columns below and in the same order. An example of an input csv can be found here
+The input csv must have all columns below and in the same order. An example of an input csv can be found here
input_csv |
yes | path | -Absolute path to the input csv. See here for example and above for the detail of required fields. | +Absolute path to the input csv. See here for example and above for the detail of required fields. |
reference_fasta_bwa |
diff --git a/development/license/index.html b/development/license/index.html
index 10cdc56..a198b23 100644
--- a/development/license/index.html
+++ b/development/license/index.html
@@ -102,7 +102,7 @@