Skip to content

Commit

Permalink
Merge pull request #397 from BU-ISCIII/develop
Browse files Browse the repository at this point in the history
Develop merge for 2.2.5 release
  • Loading branch information
victor5lm authored Jan 9, 2025
2 parents b6916d5 + d388dce commit 9d921dc
Show file tree
Hide file tree
Showing 49 changed files with 304 additions and 1,141 deletions.
37 changes: 37 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,43 @@ All notable changes to this project will be documented in this file.

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [2.2.5] - 2025-01-09 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.5

### Credits

- [Victor Lopez](https://github.com/victor5lm)

### Template fixes and updates

- Changed mag.md by taxprofiler.md in assets/reports [#396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Modified irma_output.md to include only taxprofiler [#396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Updated services.json with taxprofiler [#396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Created a lablog file for chewbbaca/REFERENCES [#396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Updated lablog_irma and renamed ANALYSIS01 folders [#396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Updated IRMA template and its files to include RSV [#396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Updated chewbbaca results' lablog to include cgMLST_MSA.fasta [#396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Updated exometrio and wgstrio results lablogs not to include exomiser's html [#396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Created plasmidid's results lablog [#396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Updated mtbseq's lablog to remove unnecessary single quotes [#396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Fixed snippy's lablog to be better explained and updated its results' lablog [#396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Updated version in pyproject.toml and __main__.py [#396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).

### Modules

#### Added enhancements

#### Fixes

#### Changed

- Replaced setup.py by pyproject.toml [#396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).

#### Removed

- Removed MAG template and replaced it with taxprofiler [#396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).

### Requirements

## [2.2.4] - 2024-12-27 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.4

### Credits
Expand Down
2 changes: 1 addition & 1 deletion bu_isciii/__main__.py
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ def run_bu_isciii():
)

# stderr.print("[green] `._,._,'\n", highlight=False)
__version__ = "2.2.4"
__version__ = "2.2.5"
stderr.print(
"[grey39] BU-ISCIII-tools version {}".format(__version__), highlight=False
)
Expand Down

Large diffs are not rendered by default.

4 changes: 2 additions & 2 deletions bu_isciii/assets/reports/results/irma_output.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,9 @@

This markdown briefly describes the files found in `RESULTS/` folder for IRMA services. As described [here]()

## **`krona_results.html`**
## **`taxprofiler`**

Includes the multiQC html report from MAG, you can find a further description in [MAG](https://github.com/BU-ISCIII/buisciii-tools/blob/main/bu_isciii/assets/reports/md/mag.md).
Includes the results from Taxprofiler, you can find a further description in [Taxprofiler](https://github.com/BU-ISCIII/buisciii-tools/blob/main/bu_isciii/assets/reports/md/taxprofiler.md).

## Files in `fragment_name/`

Expand Down
26 changes: 0 additions & 26 deletions bu_isciii/assets/reports/results/mag.md

This file was deleted.

9 changes: 9 additions & 0 deletions bu_isciii/assets/reports/results/taxprofiler.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
## Taxprofiler

Here we describe the results from the (nf-core/taxprofiler)[https://nf-co.re/taxprofiler/] pipeline for multispecies taxonomic classification and profiling of shorgun short- and long-read.

* `taxprofiler/multiqc_report.html​`: Final HTML report collecting numerical stats from each module executed in this pipeline.
* `taxprofiler/krona/database_*.html`: Interactive HTML files generated by Krona, displaying the results of taxonomic classification for supported tools (Kraken2, Centrifuge, Kaiju, and MALT)

> [!WARNING]
> Software's versions used in this analysis can be obtained from the `MultiQC` report.
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@

echo -e "sample_ID\tTotalReads\tMappedReads\tFlu_type\tReads_HA\tReads_MP\tReads_NA\tReads_NP\tReads_NS\tReads_PA\tReads_PB1\tReads_PB2" > irma_stats.txt
echo -e "sample_ID\tTotalReads\tMappedReads\t%MappedReads\tFlu_type\tReads_HA\tReads_MP\tReads_NA\tReads_NP\tReads_NS\tReads_PA\tReads_PB1\tReads_PB2" > irma_stats_flu.txt

cat ../samples_id.txt | while read in
do
Expand All @@ -19,16 +19,16 @@ PB2=$(grep '4-[A-C]_PB2' ${in}/tables/READ_COUNTS.txt | cut -f2)
#In case of Influenza C in samples:
HE=$(grep '4-C_HE' ${in}/tables/READ_COUNTS.txt | cut -f2)
if [[ -n "$HE" ]]; then
LINE=$(paste <(echo $SAMPLE_ID) <(echo $TOTAL_READS) <(echo $MAPPEDREADS) <(echo $FLU_TYPE) <(echo $HA) <(echo $MP) <(echo $NA) <(echo $NP) <(echo $NS) <(echo $PA) <(echo $PB1) <(echo $PB2) <(echo $HE))
LINE=$(paste <(echo $SAMPLE_ID) <(echo $TOTAL_READS) <(echo $MAPPEDREADS) <(echo $PCTMAPPED) <(echo $FLU_TYPE) <(echo $HA) <(echo $MP) <(echo $NA) <(echo $NP) <(echo $NS) <(echo $PA) <(echo $PB1) <(echo $PB2) <(echo $HE))
else
LINE=$(paste <(echo $SAMPLE_ID) <(echo $TOTAL_READS) <(echo $MAPPEDREADS) <(echo $FLU_TYPE) <(echo $HA) <(echo $MP) <(echo $NA) <(echo $NP) <(echo $NS) <(echo $PA) <(echo $PB1) <(echo $PB2))
LINE=$(paste <(echo $SAMPLE_ID) <(echo $TOTAL_READS) <(echo $MAPPEDREADS) <(echo $PCTMAPPED) <(echo $FLU_TYPE) <(echo $HA) <(echo $MP) <(echo $NA) <(echo $NP) <(echo $NS) <(echo $PA) <(echo $PB1) <(echo $PB2))
fi

echo "$LINE" >> irma_stats.txt
echo "$LINE" >> irma_stats_flu.txt

done

ANY_C=$(grep "C_" irma_stats.txt)
ANY_C=$(grep "C_" irma_stats_flu.txt)
if [[ -n "$ANY_C" ]]; then
sed -i 's/Reads_PB2/Reads_PB2\tReads_HE/g' irma_stats.txt
sed -i 's/Reads_PB2/Reads_PB2\tReads_HE/g' irma_stats_flu.txt
fi
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
echo -e "Sample_ID\tTotalReads\tMappedReads\t%MappedReads\tRSV_type" > irma_stats_rsv.txt

cat ../samples_id.txt | while read in
do
SAMPLE_ID=$(echo ${in})
TOTAL_READS=$(grep '1-initial' ${in}/tables/READ_COUNTS.txt | cut -f2)
MAPPEDREADS=$(grep '3-match' ${in}/tables/READ_COUNTS.txt | cut -f2)
PCTMAPPED=$(awk "BEGIN {printf \"%.2f\", ($MAPPEDREADS/$TOTAL_READS)*100}")
RSV_TYPE=$(grep '4-RSV_' ${in}/tables/READ_COUNTS.txt | cut -f1 | cut -d '_' -f2)
echo -e "${SAMPLE_ID}\t${TOTAL_READS}\t${MAPPEDREADS}\t${PCTMAPPED}\t${RSV_TYPE}" >> irma_stats_rsv.txt
done
Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,10 @@ mkdir logs

scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")

cat ../samples_id.txt | while read in; do echo "srun --partition short_idx --cpus-per-task 32 --mem 35000M --chdir $scratch_dir --time 01:00:00 --output logs/IRMA.${in}.%j.log /data/ucct/bi/pipelines/flu-amd/flu-amd-1.1.4/IRMA FLU_AD ../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz ${in} --external-config ../../../DOC/irma_config.sh &"; done > _01_irma.sh
cat ../samples_id.txt | while read in; do echo "srun --partition short_idx --cpus-per-task 32 --mem 35000M --chdir $scratch_dir --time 01:00:00 --output logs/IRMA.${in}.%j.log /data/ucct/bi/pipelines/flu-amd/flu-amd-1.2-0/IRMA FLU_AD ../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz ${in} --external-config ../../../DOC/irma_config.sh &"; done > _01_irma_flu.sh

echo 'bash create_irma_stats.sh' > _02_create_stats.sh
echo 'bash create_irma_stats_flu.sh' > _02_create_stats_flu.sh

echo 'bash postprocessing.sh' > _03_post_processing.sh
echo 'bash postprocessing_flu.sh' > _03_post_processing_flu.sh

echo 'sed "s/__//g" irma_stats.txt | sed "s/_\t/\t/g" > clean_irma_stats.txt' >> _03_post_processing.sh
echo 'sed "s/__//g" irma_stats_flu.txt | sed "s/_\t/\t/g" > clean_irma_stats_flu.txt' >> _03_post_processing_flu.sh
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
#module load R
#Fix pearl warning, add "export LC_ALL="en_US.UTF8" to .basrhc or run it now

mkdir logs

scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")

cat ../samples_id.txt | while read in; do echo "srun --partition short_idx --cpus-per-task 32 --mem 35000M --chdir $scratch_dir --time 01:00:00 --output logs/IRMA.${in}.%j.log /data/ucct/bi/pipelines/flu-amd/flu-amd-1.2.0/IRMA RSV ../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz ${in} --external-config ../../../DOC/irma_config.sh &"; done > _01_irma_rsv.sh

echo 'bash create_irma_stats_rsv.sh' > _02_create_stats_rsv.sh

echo 'bash postprocessing_rsv.sh' > _03_post_processing_rsv.sh
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
#CLEAN
if test -f all_samples_completo.txt; then rm all_samples_completo.txt; fi
if test -d A; then rm -rf A; fi
if test -d B; then rm -rf B; fi
if test -d AD; then rm -rf AD; fi
if test -d BD; then rm -rf BD; fi

cat ../samples_id.txt | while read sample; do
RSVTYPE=$(ls ${sample}/*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | cut -d '_' -f2 | sort -u)
mkdir -p $RSVTYPE
cat ${sample}/amended_consensus/${sample}.fa | sed 's/-/\//g' | sed "s/^>\([^/]*\)/>${RSVTYPE}\/\1/" | tee -a ${RSVTYPE}/${RSVTYPE}.txt all_samples_completo.txt > /dev/null
done
4 changes: 2 additions & 2 deletions bu_isciii/templates/IRMA/ANALYSIS/lablog_irma
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#ls ../RAW/* | tr '\/' '\t' | cut -f3 | cut -d "_" -f 1 | sort -u | grep -v "md5" > samples_id.txt
mkdir -p 00-reads
mv ANALYSIS01_FLU_IRMA $(date '+%Y%m%d')_ANALYSIS01_FLU_IRMA
cd 00-reads; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R1*.fastq.gz %_R1.fastq.gz" | bash; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R2*.fastq.gz %_R2.fastq.gz" | bash; cd -
mv ANALYSIS01_IRMA $(date '+%Y%m%d')_ANALYSIS01_IRMA
cd 00-reads; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R1*.fastq.gz %_R1.fastq.gz" | bash; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R2*.fastq.gz %_R2.fastq.gz" | bash; cd -
38 changes: 31 additions & 7 deletions bu_isciii/templates/IRMA/RESULTS/lablog_irma_results
100755 → 100644
Original file line number Diff line number Diff line change
@@ -1,10 +1,34 @@
#!/bin/bash

mkdir $(date '+%Y%m%d')_entrega01
cd $(date '+%Y%m%d')_entrega01

#Create symbolic links depending on the analysis
#Individual files
ln -s ../../ANALYSIS/*FLU_IRMA/04-irma/all_samples_completo.txt .
ln -s ../../ANALYSIS/*FLU_IRMA/04-irma/A_H* .
ln -s ../../ANALYSIS/*FLU_IRMA/04-irma/B .
ln -s ../../ANALYSIS/*FLU_IRMA/04-irma/C .
tail -n +2 ../../ANALYSIS/*_FLU_IRMA/04-irma/clean_irma_stats.txt | cut -f4 | sort | uniq -c > flu_type_summary.txt
# Setting the organism
echo "Please specify the organism that was analysed."
echo "1. FLU"
echo "2. RSV"
while true; do
read -p "Enter your choice (1 or 2): " ORGANISM
if [ "$ORGANISM" == "1" ]; then
ORGANISM="FLU"
echo "You selected $ORGANISM."
ln -s ../../ANALYSIS/*_IRMA/04-irma/all_samples_completo.txt .
ln -s ../../ANALYSIS/*_IRMA/04-irma/A_H* .
ln -s ../../ANALYSIS/*_IRMA/04-irma/B .
ln -s ../../ANALYSIS/*_IRMA/04-irma/C .
tail -n +2 ../../ANALYSIS/*_IRMA/04-irma/clean_irma_stats_flu.txt | cut -f4 | sort | uniq -c > flu_type_summary.txt
break
elif [ "$ORGANISM" == "2" ]; then
ORGANISM="RSV"
echo "You selected $ORGANISM."
ln -s ../../ANALYSIS/*_IRMA/04-irma/all_samples_completo.txt .
ln -s ../../ANALYSIS/*_IRMA/04-irma/A .
ln -s ../../ANALYSIS/*_IRMA/04-irma/B .
ln -s ../../ANALYSIS/*_IRMA/04-irma/AD .
ln -s ../../ANALYSIS/*_IRMA/04-irma/BD .
tail -n +2 ../../ANALYSIS/*_IRMA/04-irma/irma_stats_rsv.txt | cut -f5 | sort | uniq -c > rsv_type_summary.txt
break
else
echo "Invalid input. Please enter 1 or 2."
fi
done
13 changes: 13 additions & 0 deletions bu_isciii/templates/chewbbaca/REFERENCES/lablog
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
#!/bin/bash

# module load singularity

mkdir logs
scratch_dir=$(echo $PWD | sed "s/\/data\ucct/\/bi\/scratch_tmp/\/scratch/g")

# Schema creation
# WARNING: You have to indicate manually the folder in which your .fasta files are for the schema creation
echo "srun --chdir $scratch_dir --output logs/CHEWBBACA-CREATE-SCHEMA.%j.log --job-name CHEWBBACA-CREATE-SCHEMA --partition middle_idx --time 12:00:00 singularity exec --bind ${scratch_dir}/../ /data/ucct/bi/pipelines/singularity-images/chewbbaca:3.3.3--pyhdfd78af_0 chewBBACA.py CreateSchema -i ${scratch_dir}/%% -o ./created_schema --cpu 4 &" > _01_create_schema.sh

# cgMLST extraction
echo "srun --chdir $scratch_dir --output logs/CHEWBBACA-EXTRACT-CGMLST.%j.log --job-name CHEWBBACA-EXTRACT-CGMLST --partition middle_idx --time 12:00:00 singularity exec --bind ${scratch_dir}/../ /data/ucct/bi/pipelines/singularity-images/chewbbaca:3.3.3--pyhdfd78af_0 chewBBACA.py ExtractCgMLST -i ${scratch_dir}/../ANALYSIS/*/*-chewbbaca/allele_calling/results_alleles.tsv -o ./results_cgmlst &" > _02_extract_cgmlst.sh
3 changes: 2 additions & 1 deletion bu_isciii/templates/chewbbaca/RESULTS/lablog_mlst_results
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
DELIVERY_FOLDER="$(date '+%Y%m%d')_entrega"
DELIVERY_FOLDER="$(date '+%Y%m%d')_entrega01"

mkdir -p $DELIVERY_FOLDER
mkdir $DELIVERY_FOLDER/mlst
Expand All @@ -10,5 +10,6 @@ cd $DELIVERY_FOLDER/mlst
ln -s ../../../ANALYSIS/*CHEWBBACA/*-chewbbaca/allele_calling_evaluation/allelecall_report.html .
ln -s ../../../ANALYSIS/*CHEWBBACA/*-chewbbaca/allele_calling_evaluation/distance_matrix_symmetric.tsv .
ln -s ../../../ANALYSIS/*CHEWBBACA/*-chewbbaca/allele_calling_evaluation/results_alleles.tsv .
ln -s ../../../ANALYSIS/*CHEWBBACA/*-chewbbaca/allele_calling_evaluation/cgMLST_MSA.fasta .
ln -s ../../../ANALYSIS/*CHEWBBACA/*-grapetree/*.nwk
ln -s ../../../ANALYSIS/*CHEWBBACA/*-grapetree/*.svg
Original file line number Diff line number Diff line change
Expand Up @@ -13,15 +13,15 @@ mkdir -p logs
#-----------------------------------------------------------------------------------------------------

# 1 . Lablog to modify VCF ID field before running VEP.
echo "awk 'BEGIN{FS=\"\t\";OFS=\"\t\"} {if( \$0 ~ /^#/ ){print \$0}else{printf \"%s\t%s\t%s\t\", \$1,\$2,\$1\"_\"\$2\"_\"\$4\"_\"\$5 ; for (i=4; i<=NF; i++){printf \"%s\t\",\$i} ; printf \"\n\"}}' ../02-postprocessing/variants_fil.vcf > ./vep/variants_fil_mod.vcf" > aux_01_bcftools_query.sh
echo "sed -i 's/\t$//' ./vep/variants_fil_mod.vcf" >> aux_01_bcftools_query.sh
echo "awk 'BEGIN{FS=\"\t\";OFS=\"\t\"} {if( \$0 ~ /^#/ ){print \$0}else{printf \"%s\t%s\t%s\t\", \$1,\$2,\$1\"_\"\$2\"_\"\$4\"_\"\$5 ; for (i=4; i<=NF; i++){printf \"%s\t\",\$i} ; printf \"\n\"}}' ../02-postprocessing/variants_fil.vcf > ./vep/variants_fil_mod.vcf" > _01_bcftools_query.sh
echo "sed -i 's/\t$//' ./vep/variants_fil_mod.vcf" >> _01_bcftools_query.sh

# 2. Create variant table.

echo "singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/bcftools:1.12--h45bccc9_1 bcftools query -H -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\t%FILTER\t[%GT\t%DP\t%AD\t%GQ\t]\n' ${scratch_dir}/vep/variants_fil_mod.vcf > ${scratch_dir}/vep/variants.table" >> aux_01_bcftools_query.sh
echo "sed -i -r 's/(#|\[[0-9]+\])//g' ./vep/variants.table;sed -i 's/:/_/g' ./vep/variants.table;sed -i 's/ //g' ./vep/variants.table;sed -i 's/\t*$//g' ./vep/variants.table " >> aux_01_bcftools_query.sh
echo "singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/bcftools:1.12--h45bccc9_1 bcftools query -H -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\t%FILTER\t[%GT\t%DP\t%AD\t%GQ\t]\n' ${scratch_dir}/vep/variants_fil_mod.vcf > ${scratch_dir}/vep/variants.table" >> _01_bcftools_query.sh
echo "sed -i -r 's/(#|\[[0-9]+\])//g' ./vep/variants.table;sed -i 's/:/_/g' ./vep/variants.table;sed -i 's/ //g' ./vep/variants.table;sed -i 's/\t*$//g' ./vep/variants.table " >> _01_bcftools_query.sh

echo "srun --partition short_idx --time 2:00:00 --chdir ${scratch_dir} --output logs/BCFTOOLSQUERY.log --job-name BCFTOOLSQUERY bash ./aux_01_bcftools_query.sh &" > _01_run_bcftools_query.sh
echo "srun --partition short_idx --time 2:00:00 --chdir ${scratch_dir} --output logs/BCFTOOLSQUERY.log --job-name BCFTOOLSQUERY bash ./_01_bcftools_query.sh &" > _01_run_bcftools_query.sh

#------------------------------------------------------------------------------------------------------

Expand Down Expand Up @@ -79,15 +79,15 @@ echo "srun --partition short_idx --mem 100G --time 2:00:00 --chdir /data/ucct/bi

## Lablog to modify the output reported by exomiser and create a final file with a personalized format.
# Grep variant id for each inheritance model
cat inheritance_types.txt | xargs -I % echo "grep 'PASS' ./exomiser/exomiser_%.variants.tsv | awk '{print \$1\"_\"\$2\"_\"\$3\"_\"\$4}' > ./id_%.txt " >> _05_filter_heritance.sh
cat inheritance_types.txt | xargs -I % echo "grep 'PASS' ./exomiser/exomiser_%.variants.tsv | awk '{print \$1\"_\"\$2\"_\"\$3\"_\"\$4}' > ./id_%.txt " >> _05_filter_inheritance.sh

# Grep variants for each inheritance models from the full annotated variants file
cat inheritance_types.txt | xargs -I % echo "grep -f ./id_%.txt ./variants_annot_all.tab > ./vep_annot_%.txt" >> _05_filter_heritance.sh
cat inheritance_types.txt | xargs -I % echo "grep -f ./id_%.txt ./variants_annot_all.tab > ./vep_annot_%.txt" >> _05_filter_inheritance.sh

cat inheritance_types.txt | xargs -I % echo "cat header_vep_final_annot.txt ./vep_annot_%.txt > ./vep_annot_%_final.txt" >> _05_filter_heritance.sh
cat inheritance_types.txt | xargs -I % echo "cat header_vep_final_annot.txt ./vep_annot_%.txt > ./vep_annot_%_final.txt" >> _05_filter_inheritance.sh

echo "rm id_*" >> _05_filter_heritance.sh
cat inheritance_types.txt | xargs -I % echo "rm ./vep_annot_%.txt" >> _05_filter_heritance.sh
echo "rm id_*" >> _05_filter_inheritance.sh
cat inheritance_types.txt | xargs -I % echo "rm ./vep_annot_%.txt" >> _05_filter_inheritance.sh

# annot_all table is huge, lets shrink it a little bit
echo "srun --partition short_idx --chdir ${scratch_dir} --output logs/COMPRESS_ALL.log --job-name COMPRESS_ANNOT_ALL gzip variants_annot_all.tab &" >> _05_filter_heritance.sh
echo "srun --partition short_idx --chdir ${scratch_dir} --output logs/COMPRESS_ALL.log --job-name COMPRESS_ANNOT_ALL gzip variants_annot_all.tab &" >> _05_filter_inheritance.sh
3 changes: 0 additions & 3 deletions bu_isciii/templates/exometrio/RESULTS/lablog_exome_results
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,3 @@ ln -s ../../ANALYSIS/*ANALYSIS01_EXOME/03-annotation/variants_*filterAF*.tab .
mkdir annotation_tables
cd annotation_tables; ln -s ../../../ANALYSIS/*ANALYSIS01_EXOME/03-annotation/vep_annot*.txt . ; cd -

# For exomeEB services
# ln -s ../../ANALYSIS/*ANALYSIS01_EXOME/03-annotation/exomiser/exomiser.html .

This file was deleted.

Loading

0 comments on commit 9d921dc

Please sign in to comment.