# Title goes here

## Here's a subtitle

Here's some text explaining the command I'm trying to run

ls /lustre/scratch/joh97948/plastid_elle/half_volume_reads

## FastP

Here's the [link to the tool I'm using](https://github.com/OpenGene/fastp)

Running one sample

fastp -I /lustre/scratch/joh97948/plastid_elle/half_volume_reads/ABRONIAseq068*R1_001.fastq.gz -i  /lustre/scratch/joh97948/plastid_elle/half_volume_reads/ABRONIAseq068*R2_001.fastq.gz -O ABRONIAseq068.trimmed.R1.fastq.gz -o ABRONIAseq068.trimmed.R2.fastq.gz -j ABRONIAseq068.json -h ABRONIAseq068.html

fastp -I /lustre/scratch/joh97948/plastid_elle/tenth_volume_reads/ABRONIAseq068*R1_001.fastq.gz -i  /lustre/scratch/joh97948/plastid_elle/tenth_volume_reads/ABRONIAseq070*R2_001.fastq.gz -O ABRONIAseq070.trimmed.R1.fastq.gz -o ABRONIAseq068.trimmed.R2.fastq.gz -j ABRONIAseq068.json -h ABRONIAseq068.html

fastp -I /lustre/scratch/joh97948/plastid_elle/tenth_volume_reads/ABRONIAseq068*R1_001.fastq.gz -i  /lustre/scratch/joh97948/plastid_elle/tenth_volume_reads/ABRONIAseq070*R2_001.fastq.gz -O ABRONIAseq071.trimmed.R1.fastq.gz -o ABRONIAseq071.trimmed.R2.fastq.gz -j ABRONIAseq071.json -h ABRONIAseq071.html

Running one sample but define the name first:

name=VIOLAseq004
fastp -I /lustre/scratch/joh97948/plastid_elle/tenth_volume_reads/VIOLAseq005_M.1.trimmed.fastq.gz -i  /lustre/scratch/joh97948/plastid_elle/tenth_volume_reads/VIOLAseq005_M.2.trimmed.fastq.gz -O VIOLAseq005.trimmed_M.1.fastq.gz -o VIOLAseq005.trimmed.R2.fastq.gz -j VIOLAseq005.json -h VIOLAseq005.html

name=ABRONIAseq071
fastp -i /lustre/scratch/joh97948/plastid_elle/tenth_volume_reads/ABRONIAseq071_S756_L002_R1_001.fastq.gz -I  /lustre/scratch/joh97948/plastid_elle/tenth_volume_reads/ABRONIAseq071_S756_L002_R2_001.fastq.gz -o ABRONIAseq071_R1.trimmed.fastq.gz -O ABRONIAseq071.trimmed_R2.fastq.gz -j ABRONIAseq071.json -h ABRONIAseq071.html


ABRONIAseq071_S756_L002_R1_001
fastp -i /lustre/scratch/joh97948/plastid_elle/tenth_volume_reads/ABRONIAseq071_S756_L002_R1_001.fastq.gz -I /lustre/scratch/joh97948/plastid_elle/tenth_volume_reads/ABRONIAseq071_S756_L002_R2_001.fastq.gz -o ABRONIAseq071.trimmed_R1.fastq.gz -O ABRONIAseq071.trimmed_R2.fastq.gz -j ABRONIAseq071.json -h ABRONIAseq071.html

Loop Attempt
[help](https://stackoverflow.com/questions/1521462/looping-through-the-content-of-a-file-in-bash)

#clean up data
while read name; do fastp -I /lustre/research/joh97948/Abronia/$name_R1_001.fastq.gz -i  /lustre/research/joh97948/Abronia/$name_R2_001.fastq.gz -O $name.trimmed_R1.fastq.gz -o $name.trimmed_R2.fastq.gz -j $name.json -h $name.html; done </lustre/scratch/eliostev/samlist.txt


#read all names in samplelist.txt
for word in $(/lustre/scratch/joh97948/plastid_elle/samplelist.txt); do echo $word; done

while read name; do
    fastp \
        -i /lustre/research/joh97948/Abronia/${name}_R1_001.fastq.gz \
        -I /lustre/research/joh97948/Abronia/${name}_R2_001.fastq.gz \
        -o ${name}.trimmed_R1.fastq.gz \
        -O ${name}.trimmed_R2.fastq.gz \
        -j ${name}.json \
        -h ${name}.html
done < /lustre/scratch/eliostev/samlist.txt


while read name; do
    fastp \
        -i /lustre/research/joh97948/Abronia/${name}_R1_001.fastq.gz \
        -I /lustre/research/joh97948/Abronia/${name}_R2_001.fastq.gz \
        -o ${name}.trimmed_R1.fastq.gz \
        -O ${name}.trimmed_R2.fastq.gz \
        -j ${name}.json \
        -h ${name}.html
done < /home/eliostev/seqlistJAN.txt

Loop with Hybpiper

hybpiper assemble -t_aa /lustre/scratch/joh97948/plastid_elle/plastid_targets.faa -r ABRONIAseq070.trimmed.R*.fastq.gz --prefix ABRONIAseq070 --diamond

while read name; 
do hybpiper assemble -t_aa /lustre/scratch/joh97948/plastid_elle/plastid_targets.faa -r $name*.trimmed_R*.fastq.gz --prefix $name --diamond; done </lustre/scratch/joh97948/plastid_elle/samplelist.txt

Loop with Hybpiper 2

hybpiper assemble -t_aa /lustre/scratch/joh97948/plastid_elle/plastid_targets.faa -r ABRONIAseq070.trimmed.R*.fastq.gz --prefix ABRONIAseq070 --diamond

hybpiper assemble -t_aa /lustre/scratch/madbullo/LibMin/plastid_targets.faa -r ABRONIAseq071.R*.paired.fastq.gz --prefix ABRONIAseq071 --diamond


while read name; 
do hybpiper assemble -t_aa /lustre/scratch/madbullo/LibMin/plastid_targets.faa -r $name*.R*.paired.fastq.gz --prefix $name --diamond; done </home/eliostev/seqlistJAN.txt

submit job

# hybpiper_loop.sh
# cp - copy
mkdir slurms #make directory slurms
cd slurms #access
nano hybpiper_loop.sh #use workspace to write loop
#edit, etc.
sbatch hybpiper_loop.sh #submit job
squeue -u eliostev #check jobs

#or 
cd /lustre/scratch/eliostev
ls #make sure is correct
sbatch ~/slurms/hybpiper_loop.sh

#cancel job
scancel #job id here

run stats!

hybpiper stats -t_aa /lustre/scratch/joh97948/plastid_elle/plastid_targets.faa gene /lustre/scratch/eliostev/halfVol_results/samplelist.txt

hybpiper stats -t_aa /lustre/scratch/joh97948/plastid_elle/plastid_targets.faa gene /lustre/scratch/eliostev/samplelist2.txt

hybpiper stats -t_aa /lustre/scratch/madbullo/LibMin/plastid_targets.faa gene /lustre/scratch/eliostev/seqlistJAN.txt

/lustre/work/joh97948/angiosperms353.abronia.fasta <-- target file
while read name; do
    fastp \
        -i /lustre/research/joh97948/Abronia/${name}_M.1.trimmed.fastq.gz \
        -I /lustre/research/joh97948/Abronia/${name}_M.2.trimmed.fastq.gz \
        -o ${name}.trimmed_R1.fastq.gz \
        -O ${name}.trimmed_R2.fastq.gz \
        -j ${name}.json \
        -h ${name}.html
done < /lustre/scratch/joh97948/plastid_elle/samplelist.txt

average length --- 

#!/bin/bash

indir="/lustre/scratch/eliostev/abronia/Abronia"
outdir="/lustre/scratch/eliostev/trimmed"

mkdir -p "$outdir"

while read -r name; do
    R1=$(ls ${indir}/${name}*_R1_001.fastq.gz 2>/dev/null | head -n1)
    R2=$(ls ${indir}/${name}*_R2_001.fastq.gz 2>/dev/null | head -n1)

    if [[ -z "$R1" || -z "$R2" ]]; then
        echo "pairs not found: $name"
        continue
    fi

    fastp \
        -i "$R1" \
        -I "$R2" \
        -o ${outdir}/${name}.trimmed_R1.fastq.gz \
        -O ${outdir}/${name}.trimmed_R2.fastq.gz \
        -j ${outdir}/${name}.json \
        -h ${outdir}/${name}.html

done < /lustre/scratch/eliostev/samlist2.txt