Merge pull request #2 from McMinds-Lab/main

start fresh for soil edna starting files

.gitignore

@@ -2,3 +2,4 @@
 *.env
 *DS_Store
 .Rapp.history
+*.hpp

microbiomes/qc_amplicons/01_init_QC.sh

@@ -0,0 +1,67 @@
+# get local variables
+source local.env
+
+mkdir -p ${outdir}/01_init_QC
+
+cat <<EOF > ${outdir}/01_init_QC/01_init_QC.sbatch
+#!/bin/bash
+#SBATCH --job-name=01_init_QC
+#SBATCH --partition=${partition}
+#SBATCH --qos=${qos}
+#SBATCH --mail-user=${email}
+#SBATCH --mail-type=END,FAIL
+#SBATCH --output=${outdir}/01_init_QC/01_init_QC.log
+#SBATCH --ntasks=${nthreads}
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=20
+#SBATCH --time=01:00:00
+
+# get local variables
+source local.env
+
+mkdir -p ${outdir}/01_init_QC/demultiplexed/
+mkdir -p ${outdir}/01_init_QC/merged
+
+# trim indices and primers from sequences, demultiplex, and discard any sequences that don't contain both full barcodes and primers
+module purge
+module load hub.apps/anaconda3
+source activate cutadapt
+cutadapt \
+  --no-indels \
+  --discard-untrimmed \
+  --pair-filter=any \
+  -g file:${barcodes_fwd} \
+  -G file:${barcodes_rev} \
+  -o ${outdir}/01_init_QC/demultiplexed/{name1}-{name2}_R1.fastq \
+  -p ${outdir}/01_init_QC/demultiplexed/{name1}-{name2}_R2.fastq \
+  ${in_fwd} \
+  ${in_rev}
+# double check that reads are oriented consistently (does the above need to be re-run with the forward and reverse indices and or primers switched?)
+
+for file in ${outdir}/01_init_QC/demultiplexed/*_R1.fastq; do
+
+  # trim "R1" from filenames to get Sample IDs that match mapping file
+  filename=\$(basename \$file)
+  sampleid=\${filename/-*/} ## double check that all files have matching name1 and name2 or else this could overwrite a good file with a bad one
+
+  # merge paired-end reads such that short reads, where the read is longer than the insertion (such as mitochondria), are not discarded, and nucleotides are trimmed that extend past the beginning of the paired read (which are just adaptor sequences)
+
+  conda deactivate
+  module purge
+  module load apps/vsearch
+  vsearch \
+    --fastq_mergepairs \${file} \
+    --reverse \${file/R1/R2} \
+    --fastq_allowmergestagger \
+    --fasta_width 0 \
+    --threads ${nthreads} \
+    --fastqout ${outdir}/01_init_QC/merged/\${sampleid}.fastq
+
+done
+
+EOF
+
+if $autorun; then
+    sbatch ${outdir}/01_init_QC/01_init_QC.sbatch
+fi

microbiomes/qc_amplicons/02_dada2.r

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+library(dada2)
+
+#do dada2 stuff

microbiomes/qc_amplicons/02_dada2.sh

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+# get local variables
+source local.env
+
+mkdir -p ${outdir}/02_dada2
+
+cat <<EOF > ${outdir}/02_dada2/02_dada2.sbatch
+#!/bin/bash
+#SBATCH --job-name=02_dada2
+#SBATCH --partition=${partition}
+#SBATCH --qos=${qos}
+#SBATCH --mail-user=${email}
+#SBATCH --mail-type=END,FAIL
+#SBATCH --output=${outdir}/02_dada2/02_dada2.log
+#SBATCH --ntasks=${nthreads}
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=20
+#SBATCH --time=01:00:00
+
+module load apps/R
+Rscript 02_dada2.r
+
+EOF
+
+if $autorun; then
+    sbatch ${outdir}/01_init_QC/01_init_QC.sbatch
+fi

microbiomes/qc_amplicons/README

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+make a copy of local.env.txt to local.env and fill in the blanks
+
+run each script by changing into this directory and then using 'bash scriptname.sh'. If 'autorun=true' in the local.env file, this will internally submit an sbatch command

microbiomes/qc_amplicons/local.env.txt

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+[email protected]
+
+## how many processors do you want to use
+nthreads=20
+
+## max ram
+maxram=20G
+
+## what slurm partition and qos do you want to use
+partition=rra
+qos=rra
+
+in_fwd=
+in_rev=
+barcodes_fwd=barcodes_fwd.fasta
+barcodes_rev=barcodes_rev.fasta
+outdir=/path/to/output/directory
+
+autorun=true
+
+## this tells the scripts where to find this file
+scriptdir=$(dirname "$(realpath -s "$0")")