fix: update command arguments in workflow tests and correct primer file reference

Author: lewisl23

.github/.DS_Store

@@ -18,7 +18,7 @@ jobs:
 
       - name: Test container presto-0.7.4:latest runs
         run: |
-          docker run --rm ghcr.io/lewisl23/presto-0.7.4:latest "AssemblePairs.py --help"
+          docker run --rm ghcr.io/lewisl23/presto-0.7.4:latest AssemblePairs.py --help
           echo "Container works"
         
       - name: Pull container igblast-1.21.0:latest from GHCR
@@ -27,5 +27,5 @@ jobs:
 
       - name: Test container igblast-1.21.0:latest runs
         run: |
-          docker run --rm ghcr.io/lewisl23/igblast-1.21.0:latest "igblastn -help"
+          docker run --rm ghcr.io/lewisl23/igblast-1.21.0:latest igblastn -help
           echo "Container works"

.github/workflows/main.yml

@@ -1,6 +1,12 @@
 # Raw2AIRR
-
+### #This tool is initially created for MSc dissertation project "BCR_classification_model"
 Raw2AIRR is a bioinformatic pipeline that is used to process raw illumina reads 
 of B-cell receptor (BCR). The tool will will start from undergoing paired-end 
 assemble, quality-control, and collapse of duplicated reads. Then, the reads 
 undergo alignment and annotation with OGRDB database to transform the reads into machine readable standardised file that represents the adaptive immune receptor repertoire data.
+
+Note: Please configure according to the sequencing method\
+1. PRIMERS used for the sequencing should be configured using "presto/Primers.fasta"
+2. Sample name should be configured using "/snakeconfig.yaml"
+
+what

README.md

@@ -52,7 +52,7 @@ rule filter:
 rule mask_primer:
     input:
         reads = "presto/presto_output/{sample}_quality-pass.fastq"
-        primer = "presto/Cowan_CPrimers.fasta"
+        primer = "presto/Primers.fasta"
     output:
         pass_file = "presto/presto_output/{sample}_primers-pass.fastq"
     container: