From 8911a6f7eff40331b0d207228404c9fb6842d98f Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawar@subcom.tech>
Date: Sat, 30 Jul 2022 15:29:40 +0530
Subject: [PATCH] Added the pipeline.

Run `copr .`
---
 data/non-curated/SampleInputFileLinks.txt       |  12 ------------
 .../TrainingDataSet_Process_Codes.xlsx          | Bin 11017 -> 0 bytes
 vendor/shodhka/test_20220727/README.md          |  15 ++++++++++-----
 vendor/shodhka/test_20220727/run.copr.sh        |  11 +++++++++++
 4 files changed, 21 insertions(+), 17 deletions(-)
 delete mode 100644 data/non-curated/SampleInputFileLinks.txt
 delete mode 100644 data/non-curated/TrainingDataSet_Process_Codes.xlsx
 create mode 100755 vendor/shodhka/test_20220727/run.copr.sh

diff --git a/data/non-curated/SampleInputFileLinks.txt b/data/non-curated/SampleInputFileLinks.txt
deleted file mode 100644
index 0c16ca5..0000000
--- a/data/non-curated/SampleInputFileLinks.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-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
diff --git a/data/non-curated/TrainingDataSet_Process_Codes.xlsx b/data/non-curated/TrainingDataSet_Process_Codes.xlsx
deleted file mode 100644
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diff --git a/vendor/shodhka/test_20220727/README.md b/vendor/shodhka/test_20220727/README.md
index 619539f..beb34db 100644
--- a/vendor/shodhka/test_20220727/README.md
+++ b/vendor/shodhka/test_20220727/README.md
@@ -1,5 +1,10 @@
-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
diff --git a/vendor/shodhka/test_20220727/run.copr.sh b/vendor/shodhka/test_20220727/run.copr.sh
new file mode 100755
index 0000000..c265cdf
--- /dev/null
+++ b/vendor/shodhka/test_20220727/run.copr.sh
@@ -0,0 +1,11 @@
+#!/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
-- 
GitLab