Get rid of separate script file

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/lesson1/rnaseq_analysis_on_input_file.sh b/lesson1/rnaseq_analysis_on_input_file.sh
deleted file mode 100755 (executable)
index 1996706..0000000
--- a/lesson1/rnaseq_analysis_on_input_file.sh
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/bin/bash
-
-# Based on
-# https://hbctraining.github.io/Intro-to-rnaseq-hpc-O2/lessons/07_automating_workflow.html
-#
-
-# This script takes a fastq file of RNA-Seq data, runs FastQC and outputs a counts file for it.
-# USAGE: sh rnaseq_analysis_on_input_file.sh <name of fastq file>
-
-set -e
-
-# initialize a variable with an intuitive name to store the name of the input fastq file
-fq=$1
-
-# grab base of filename for naming outputs
-base=`basename $fq .subset.fq`
-echo "Sample name is $base"
-
-# specify the number of cores to use
-cores=4
-
-# directory with genome reference FASTA and index files + name of the gene annotation file
-genome=rnaseq/reference_data
-gtf=rnaseq/reference_data/chr1-hg19_genes.gtf
-
-# make all of the output directories
-# The -p option means mkdir will create the whole path if it
-# does not exist and refrain from complaining if it does exist
-mkdir -p rnaseq/results/fastqc
-mkdir -p rnaseq/results/STAR
-mkdir -p rnaseq/results/counts
-
-# set up output filenames and locations
-fastqc_out=rnaseq/results/fastqc
-align_out=rnaseq/results/STAR/${base}_
-counts_input_bam=rnaseq/results/STAR/${base}_Aligned.sortedByCoord.out.bam
-counts=rnaseq/results/counts/${base}_featurecounts.txt
-
-echo "Processing file $fq"
-
-# Run FastQC and move output to the appropriate folder
-fastqc $fq
-
-# Run STAR
-STAR --runThreadN $cores --genomeDir $genome --readFilesIn $fq --outFileNamePrefix $align_out --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard
-
-# Create BAM index
-samtools index $counts_input_bam
-
-# Count mapped reads
-featureCounts -T $cores -s 2 -a $gtf -o $counts $counts_input_bam