-
Notifications
You must be signed in to change notification settings - Fork 3
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
6 changed files
with
143 additions
and
14 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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| #!/bin/bash | ||
|
|
||
| FILE=${1} | ||
| #LIST=$2 | ||
|
|
||
| #STAT=$(basename $(basename ${LIST}) .txt) | ||
| echo "Filename"$'\t'"Total"$'\t'"mapped_reads"$'\t'"unmapped_reads"$'\t'"proportion_mapped"$'\t'"proportion_unmapped" > ${FILE}.mappedstats.txt | ||
|
|
||
|
|
||
| mapped_reads=$(samtools stats ${FILE}.sorted.bam | grep ^SN | awk 'NR == 7 {print $4}') | ||
| unmapped_reads=$(samtools stats ${FILE}.sorted.bam | grep ^SN | awk 'NR == 9 {print $4}') | ||
| total=$(samtools stats ${FILE}.sorted.bam | grep ^SN | awk 'NR == 1 {print $5}') | ||
| proportion_mapped=$(awk "BEGIN {printf \"%.2f\n\", $mapped_reads*100/$total}") | ||
| proportion_unmapped=$(awk "BEGIN {printf \"%.2f\n\", $unmapped_reads*100/$total}") | ||
| printf "%s\t%s\t%s\t%s\t%s\t%s\n" $FILE $total $mapped_reads $unmapped_reads $proportion_mapped $proportion_unmapped >> ${FILE}.mappedstats.txt | ||
| # remove bam file | ||
| #rm -rf /MIGE/01_DATA/02_MAPPING/${FILE}*.{bam,bai} |
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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| process BAM_STATISTICS { | ||
|
|
||
| label 'minimap2' | ||
|
|
||
| publishDir ( | ||
|
|
||
| path: "${params.output}/intermediate", | ||
| mode: params.publish_dir_mode, | ||
| pattern: "*.mappedstats.txt", | ||
| enabled: !params.no_intermediate, | ||
| saveAs: { fn -> | ||
| fn.startsWith("keep_") ? "map-to-keep/${fn.replaceAll(~'^keep_', '')}" : "map-to-remove/${fn}" | ||
| } | ||
| ) | ||
|
|
||
| input: | ||
| tuple val(name), val(type), path(bam) | ||
|
|
||
|
|
||
| output: | ||
| path("*.mappedstats.txt") | ||
|
|
||
|
|
||
| script: | ||
| """ | ||
| bam_stats.sh ${name} | ||
| """ | ||
|
|
||
| stub: | ||
| """ | ||
| touch ${bam.baseName}.mappedstats.txt | ||
| """ | ||
| } | ||
|
|
||
|
|
||
| process COMBINE_BAM_STATISTICS { | ||
|
|
||
| label 'minimap2' | ||
|
|
||
| publishDir ( | ||
|
|
||
| path: "${params.output}/intermediate", | ||
| mode: params.publish_dir_mode, | ||
| pattern: "combined_bam_stats.txt", | ||
| enabled: !params.no_intermediate, | ||
| saveAs: { fn -> | ||
| fn.startsWith("keep_") ? "map-to-keep/${fn.replaceAll(~'^keep_', '')}" : "map-to-remove/${fn}" | ||
| } | ||
| ) | ||
|
|
||
| tag { 'combine bam statistics files'} | ||
|
|
||
|
|
||
| input: | ||
| path(bam_statistics_files) | ||
|
|
||
|
|
||
| output: | ||
| path("combined_bam_stats.txt") | ||
|
|
||
|
|
||
| script: | ||
| """ | ||
| BAM_STATISTICS_FILES=(${bam_statistics_files}) | ||
| for index in \${!BAM_STATISTICS_FILES[@]}; do | ||
| BAM_STATISTICS_FILE=\${BAM_STATISTICS_FILES[\$index]} | ||
| # add header line if first file | ||
| if [[ \$index -eq 0 ]]; then | ||
| echo "\$(head -1 \${BAM_STATISTICS_FILE})" >> combined_bam_stats.txt | ||
| fi | ||
| echo "\$(awk 'FNR==2 {print}' \${BAM_STATISTICS_FILE})" >> combined_bam_stats.txt | ||
| done | ||
| """ | ||
|
|
||
| stub: | ||
| """ | ||
| touch combined_bam_stats.txt | ||
| """ | ||
| } |
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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| include { BAM_STATISTICS; COMBINE_BAM_STATISTICS } from '../modules/summarize' | ||
|
|
||
| workflow summarize { | ||
|
|
||
| take: | ||
| sorted_bam | ||
|
|
||
| main: | ||
| BAM_STATISTICS(sorted_bam) | ||
|
|
||
| collected_bam_statistics_ch = BAM_STATISTICS.out.collect( sort: {a, b -> a[0].getBaseName() <=> b[0].getBaseName()} ) | ||
|
|
||
|
|
||
| COMBINE_BAM_STATISTICS(collected_bam_statistics_ch) | ||
|
|
||
| // define output | ||
| bamstats = BAM_STATISTICS.out | ||
| summarystats = COMBINE_BAM_STATISTICS.out | ||
|
|
||
| emit: | ||
| bamstats | ||
| summarystats | ||
| } |