Added the pipeline.

Run `copr .`

data/non-curated/SampleInputFileLinks.txt

-ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/096/SRR11862696/SRR11862696_1.fastq.gz
-ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/096/SRR11862696/SRR11862696_2.fastq.gz
-ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/097/SRR11862697/SRR11862697_1.fastq.gz
-ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/097/SRR11862697/SRR11862697_2.fastq.gz
-ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/099/SRR11862699/SRR11862699_1.fastq.gz
-ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/099/SRR11862699/SRR11862699_2.fastq.gz
-ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/082/SRR11862682/SRR11862682_1.fastq.gz
-ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/082/SRR11862682/SRR11862682_2.fastq.gz
-ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/091/SRR11862691/SRR11862691_1.fastq.gz
-ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/091/SRR11862691/SRR11862691_2.fastq.gz
-ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/092/SRR11862692/SRR11862692_1.fastq.gz
-ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/092/SRR11862692/SRR11862692_2.fastq.gz
\ No newline at end of file

vendor/shodhka/test_20220727/README.md

-a) Sample raw data: enclosed is a text file with dataset download links 
-b) file types for inputs and outputs at each step (particularly for FASTQC and TrimGalore (first two steps) operations): enclosed as a table below (also enclosed the corresponding excel file):
-S.No. Analysis stage Tool used Input file type Code Output data type
-1 Quality check FastQC fq / fastq ./fastqc *fastq.gz text, html QC reports
-2 Quality trimming TrimGalore fq / fastq trim_galore --gzip --fastqc --max_n 2 --paired --length 50 SRR11862696_1.fastq.gz SRR11862696_2.fastq.gz fq; fastq
+1. Sample raw data: enclosed is a text file with dataset download links.  
+2. File types for inputs and outputs at each step (particularly for FASTQC and
+TrimGalore (first two steps) operations)
+
+Enclosed as a table below (also enclosed the corresponding excel file): 
+
+S.No. Analysis stage Tool used Input file type Code Output data type 1 Quality check FastQC fq / fastq ./fastqc
+*fastq.gz text, html QC reports 2 Quality trimming TrimGalore fq / fastq
+trim_galore --gzip --fastqc --max_n 2 --paired --length 50
+SRR11862696_1.fastq.gz SRR11862696_2.fastq.gz fq; fastq

vendor/shodhka/test_20220727/run.copr.sh

+#!/usr/bin/env bash
+
+FILES=$(cat ./data/SampleInputFileLinks.txt)
+for file in $FILES; do
+    # --no-clobber, do not download if file already exists.
+    wget -nc $file
+done
+
+fastqc *fastq.gz
+trim_galore --gzip --fastqc --max_n 2 --paired --length 50 \
+     SRR11862696_1.fastq.gz SRR11862696_2.fastq.gz