Commit 96cbb25c authored by Valentina Galata's avatar Valentina Galata
Browse files

archive: scripts for results archive

parent de480bee
#!/bin/bash -l
# execute from base code directory
ARCHIVE="/scratch/users/vgalata/ONT_pilot_manuscript/results_archive/$(date +"%Y%m%d")"
mkdir -p "${ARCHIVE}"
# copy data
SAMPLES="zymo nwc gdb rumen"
# SAMPLES="zymo"
for SNAME in ${SAMPLES}; do
echo "Copy data for ${SNAME} into ${ARCHIVE}"
rsync -rtP --copy-links --prune-empty-dirs \
--include="*/" --include-from="config/archive/results_archive_incl.txt" \
--exclude="*" "/scratch/users/vgalata/${SNAME}/results/" "${ARCHIVE}/${SNAME}/"
done && \
rsync -rtP "README_ARCHIVE.md" "${ARCHIVE}/" && \
cd "$(dirname ${ARCHIVE})" && \
tar -cvf - "$(basename ${ARCHIVE})" | pigz --best -p 5 > "$(basename ${ARCHIVE}).tar.gz"
# preprocessing stats
preproc/metag/sr/fastp.html
preproc/metag/sr/fastp.tsv
preproc/metat/sr/fastp.html
preproc/metat/sr/fastp.tsv
preproc/metag/lr/bbmap.host.stats
preproc/metag/sr/bbmap.host.stats
preproc/metat/sr/bbmap.host.stats
preproc/metat/sr/bbmap.rrna.stats
# reads QC
qc/metag/sr/R1.fastp_fastqc.zip
qc/metag/sr/R2.fastp_fastqc.zip
qc/metat/sr/R1.fastp_fastqc.zip
qc/metat/sr/R2.fastp_fastqc.zip
qc/metag/lr/NanoStats.tsv
qc/metag/lr/NanoStats.txt
# assembly: raw, polished, polishing steps
assembly/hy/metaspadeshybrid/ASSEMBLY.fasta
assembly/hy/metaspadeshybrid/ASSEMBLY.POLISHED.fasta
assembly/hy/metaspadeshybrid/POLISHING_raconSR1/ASSEMBLY.fasta
assembly/hy/metaspadeshybrid/POLISHING_raconSR2/ASSEMBLY.fasta
assembly/hy/metaspadeshybrid/POLISHING_raconSR3/ASSEMBLY.fasta
assembly/hy/metaspadeshybrid/POLISHING_raconSR4/ASSEMBLY.fasta
assembly/hy/metaspadeshybrid/POLISHING_raconSR5/ASSEMBLY.fasta
assembly/hy/operamsmegahit/ASSEMBLY.fasta
assembly/hy/operamsmegahit/ASSEMBLY.POLISHED.fasta
assembly/hy/operamsmegahit/POLISHING_raconSR1/ASSEMBLY.fasta
assembly/hy/operamsmegahit/POLISHING_raconSR2/ASSEMBLY.fasta
assembly/hy/operamsmegahit/POLISHING_raconSR3/ASSEMBLY.fasta
assembly/hy/operamsmegahit/POLISHING_raconSR4/ASSEMBLY.fasta
assembly/hy/operamsmegahit/POLISHING_raconSR5/ASSEMBLY.fasta
assembly/hy/operamsmetaspades/ASSEMBLY.fasta
assembly/hy/operamsmetaspades/ASSEMBLY.POLISHED.fasta
assembly/hy/operamsmetaspades/POLISHING_raconSR1/ASSEMBLY.fasta
assembly/hy/operamsmetaspades/POLISHING_raconSR2/ASSEMBLY.fasta
assembly/hy/operamsmetaspades/POLISHING_raconSR3/ASSEMBLY.fasta
assembly/hy/operamsmetaspades/POLISHING_raconSR4/ASSEMBLY.fasta
assembly/hy/operamsmetaspades/POLISHING_raconSR5/ASSEMBLY.fasta
assembly/lr/flye/ASSEMBLY.fasta
assembly/lr/flye/ASSEMBLY.POLISHED.fasta
assembly/lr/flye/POLISHING_raconLR1/ASSEMBLY.fasta
assembly/lr/flye/POLISHING_raconLR1_raconSR1/ASSEMBLY.fasta
assembly/lr/flye/POLISHING_raconLR1_raconSR2/ASSEMBLY.fasta
assembly/lr/flye/POLISHING_raconLR1_raconSR3/ASSEMBLY.fasta
assembly/lr/flye/POLISHING_raconLR1_raconSR4/ASSEMBLY.fasta
assembly/lr/flye/POLISHING_raconLR1_raconSR4_medakaLR1/ASSEMBLY.fasta
assembly/lr/raven/ASSEMBLY.fasta
assembly/lr/raven/ASSEMBLY.POLISHED.fasta
assembly/lr/raven/POLISHING_raconLR1/ASSEMBLY.fasta
assembly/lr/raven/POLISHING_raconLR1_raconSR1/ASSEMBLY.fasta
assembly/lr/raven/POLISHING_raconLR1_raconSR2/ASSEMBLY.fasta
assembly/lr/raven/POLISHING_raconLR1_raconSR3/ASSEMBLY.fasta
assembly/lr/raven/POLISHING_raconLR1_raconSR4/ASSEMBLY.fasta
assembly/lr/raven/POLISHING_raconLR1_raconSR4_medakaLR1/ASSEMBLY.fasta
assembly/sr/megahit/ASSEMBLY.fasta
assembly/sr/metaspades/ASSEMBLY.fasta
# mapping: metag
mapping/metag/hy/metaspadeshybrid/ASSEMBLY.POLISHED.hy.bam
mapping/metag/hy/operamsmegahit/ASSEMBLY.POLISHED.hy.bam
mapping/metag/hy/operamsmetaspades/ASSEMBLY.POLISHED.hy.bam
mapping/metag/lr/flye/ASSEMBLY.POLISHED.lr.bam
mapping/metag/lr/raven/ASSEMBLY.POLISHED.lr.bam
mapping/metag/sr/megahit/ASSEMBLY.POLISHED.sr.bam
mapping/metag/sr/metaspades/ASSEMBLY.POLISHED.sr.bam
mapping/metag/mappability.tsv
# mapping: metat
mapping/metat/hy/metaspadeshybrid/ASSEMBLY.POLISHED.sr.bam
mapping/metat/hy/operamsmegahit/ASSEMBLY.POLISHED.sr.bam
mapping/metat/hy/operamsmetaspades/ASSEMBLY.POLISHED.sr.bam
mapping/metat/lr/flye/ASSEMBLY.POLISHED.sr.bam
mapping/metat/lr/raven/ASSEMBLY.POLISHED.sr.bam
mapping/metat/sr/megahit/ASSEMBLY.POLISHED.sr.bam
mapping/metat/sr/metaspades/ASSEMBLY.POLISHED.sr.bam
mapping/metat/mappability.tsv
# annotation: prodigal
annotation/prodigal/hy/metaspadeshybrid/proteins.faa
annotation/prodigal/hy/operamsmegahit/proteins.faa
annotation/prodigal/hy/operamsmetaspades/proteins.faa
annotation/prodigal/lr/flye/proteins.faa
annotation/prodigal/lr/raven/proteins.faa
annotation/prodigal/sr/megahit/proteins.faa
annotation/prodigal/sr/metaspades/proteins.faa
annotation/prodigal/summary.gene.counts.tsv
annotation/prodigal/summary.gene.length.tsv
# annotation: rgi
annotation/rgi/hy/metaspadeshybrid/rgi.txt
annotation/rgi/hy/operamsmegahit/rgi.txt
annotation/rgi/hy/operamsmetaspades/rgi.txt
annotation/rgi/lr/flye/rgi.txt
annotation/rgi/lr/raven/rgi.txt
annotation/rgi/sr/megahit/rgi.txt
annotation/rgi/sr/metaspades/rgi.txt
annotation/rgi/summary.tsv
# annotation: barrnap
annotation/barrnap/hy/metaspadeshybrid/*.gff
annotation/barrnap/hy/operamsmegahit/*.gff
annotation/barrnap/hy/operamsmetaspades/*.gff
annotation/barrnap/lr/flye/*.gff
annotation/barrnap/lr/raven/*.gff
annotation/barrnap/sr/megahit/*.gff
annotation/barrnap/sr/metaspades/*.gff
annotation/barrnap/summary.tsv
# analysis
analysis/quast/hy/metaspadeshybrid/report.tsv
analysis/quast/hy/operamsmegahit/report.tsv
analysis/quast/hy/operamsmetaspades/report.tsv
analysis/quast/lr/flye/report.tsv
analysis/quast/lr/raven/report.tsv
analysis/quast/sr/megahit/report.tsv
analysis/quast/sr/metaspades/report.tsv
analysis/quast/summary_report.tsv
analysis/mash/contigs.*
analysis/diamond/hy_metaspadeshybrid.tsv
analysis/diamond/hy_operamsmegahit.tsv
analysis/diamond/hy_operamsmetaspades.tsv
analysis/diamond/lr_flye.tsv
analysis/diamond/lr_raven.tsv
analysis/diamond/sr_megahit.tsv
analysis/diamond/sr_metaspades.tsv
analysis/diamond/summary.db.tsv
analysis/mmseqs2/clusters.tsv
analysis/mmseqs2/summary.tsv
# GDB metaP reports
metap/20210323/flye_1_1_Default_Peptide_Report.txt
metap/20210323/flye_1_1_Default_Protein_Report.txt
metap/20210323/megahit_1_1_Default_Peptide_Report.txt
metap/20210323/megahit_1_1_Default_Protein_Report.txt
metap/20210323/metaspades_1_1_Default_Peptide_Report.txt
metap/20210323/metaspades_1_1_Default_Protein_Report.txt
metap/20210323/metaspadeshybrid_1_1_Default_Peptide_Report.txt
metap/20210323/metaspadeshybrid_1_1_Default_Protein_Report.txt
metap/20210323/operamsmegahit_1_1_Default_Peptide_Report.txt
metap/20210323/operamsmegahit_1_1_Default_Protein_Report.txt
metap/20210323/operamsmetaspades_1_1_Default_Peptide_Report.txt
metap/20210323/operamsmetaspades_1_1_Default_Protein_Report.txt
metap/20210323/proteins_1_1_Default_Peptide_Report.txt
metap/20210323/proteins_1_1_Default_Protein_Report.txt
metap/20210323/raven_1_1_Default_Peptide_Report.txt
metap/20210323/raven_1_1_Default_Protein_Report.txt
# GDB extra analysis
report/amr.tsv
report/mmseqs2_highconf.tsv
report/mmseqs2_uniq.tsv
report/metap.txt
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