-
Notifications
You must be signed in to change notification settings - Fork 14
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #397 from BU-ISCIII/develop
Develop merge for 2.2.5 release
- Loading branch information
Showing
49 changed files
with
304 additions
and
1,141 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
753 changes: 0 additions & 753 deletions
753
bu_isciii/assets/reports/md/mag.md → bu_isciii/assets/reports/md/taxprofiler.md
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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. |
File renamed without changes.
File renamed without changes.
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
11 changes: 11 additions & 0 deletions
11
bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/04-irma/create_irma_stats_rsv.sh
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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 |
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
12 changes: 12 additions & 0 deletions
12
bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/04-irma/lablog_rsv
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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 ${in} --external-config ../../../DOC/irma_config.sh &"; done > _01_irma_rsv.sh | ||
|
||
echo 'bash create_irma_stats_rsv.sh' > _02_create_stats_rsv.sh | ||
|
||
echo 'bash postprocessing_rsv.sh' > _03_post_processing_rsv.sh |
File renamed without changes.
12 changes: 12 additions & 0 deletions
12
bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/04-irma/postprocessing_rsv.sh
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,12 @@ | ||
#CLEAN | ||
if test -f all_samples_completo.txt; then rm all_samples_completo.txt; fi | ||
if test -d A; then rm -rf A; fi | ||
if test -d B; then rm -rf B; fi | ||
if test -d AD; then rm -rf AD; fi | ||
if test -d BD; then rm -rf BD; fi | ||
|
||
cat ../samples_id.txt | while read sample; do | ||
RSVTYPE=$(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 |
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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
38
bu_isciii/templates/IRMA/RESULTS/lablog_irma_results
100755 → 100644
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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 $ORGANISM." | ||
ln -s ../../ANALYSIS/*_IRMA/04-irma/all_samples_completo.txt . | ||
ln -s ../../ANALYSIS/*_IRMA/04-irma/A . | ||
ln -s ../../ANALYSIS/*_IRMA/04-irma/B . | ||
ln -s ../../ANALYSIS/*_IRMA/04-irma/AD . | ||
ln -s ../../ANALYSIS/*_IRMA/04-irma/BD . | ||
tail -n +2 ../../ANALYSIS/*_IRMA/04-irma/irma_stats_rsv.txt | cut -f5 | sort | uniq -c > rsv_type_summary.txt | ||
break | ||
else | ||
echo "Invalid input. Please enter 1 or 2." | ||
fi | ||
done |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,13 @@ | ||
#!/bin/bash | ||
|
||
# module load singularity | ||
|
||
mkdir logs | ||
scratch_dir=$(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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
25 changes: 0 additions & 25 deletions
25
bu_isciii/templates/mag/ANALYSIS/ANALYSIS02_MAG_TAXONOMICS/99-stats/lablog
This file was deleted.
Oops, something went wrong.
Oops, something went wrong.