-
Notifications
You must be signed in to change notification settings - Fork 9
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 #145 from parsaeskandar/master
Haplotype sampling WDL
- Loading branch information
Showing
10 changed files
with
721 additions
and
112 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 +1,5 @@ | ||
| { | ||
| "HaplotypeSampling.IN_GBZ_FILE": "tests/small_sim_graph/graph.gbz", | ||
| "HaplotypeSampling.INPUT_READ_FILE_FIRST": "tests/small_sim_graph/reads_1.fastq.gz", | ||
| "HaplotypeSampling.INPUT_READ_FILE_SECOND": "tests/small_sim_graph/reads_2.fastq.gz" | ||
| } |
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 +1,14 @@ | ||
| { | ||
| "Giraffe.INPUT_READ_FILE_1": "tests/small_sim_graph/reads_1.fastq.gz", | ||
| "Giraffe.INPUT_READ_FILE_2": "tests/small_sim_graph/reads_2.fastq.gz", | ||
| "Giraffe.GBZ_FILE": "tests/small_sim_graph/graph.gbz", | ||
| "Giraffe.REFERENCE_PREFIX": "chr", | ||
| "Giraffe.SAMPLE_NAME": "s0", | ||
| "Giraffe.MIN_FILE": "tests/small_sim_graph/graph.min", | ||
| "Giraffe.DIST_FILE": "tests/small_sim_graph/graph.dist", | ||
| "Giraffe.OUTPUT_GAF": true, | ||
| "Giraffe.OUTPUT_CALLING_BAMS": true, | ||
| "Giraffe.OUTPUT_SINGLE_BAM": true, | ||
| "Giraffe.MAP_MEM": 8, | ||
| "Giraffe.HAPLOTYPE_SAMPLING": true | ||
| } |
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 |
|---|---|---|
|
|
@@ -4,3 +4,5 @@ | |
| "HappyEvaluation.REFERENCE_FILE": "tests/small_sim_graph/ref.fa", | ||
| "HappyEvaluation.REMOVE_HOM_REFS": true | ||
| } | ||
|
|
||
|
|
||
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 +1,162 @@ | ||
| version 1.0 | ||
|
|
||
|
|
||
| task createDistanceIndex { | ||
| input { | ||
| File in_gbz_file | ||
| Int nb_cores = 16 | ||
| Int in_extract_mem = 120 | ||
| Int in_extract_disk = 2 * round(size(in_gbz_file, "G")) + 20 | ||
| } | ||
| String output_prefix = sub(basename(in_gbz_file), "\\.gbz$", "") | ||
|
|
||
| command { | ||
| set -eux -o pipefail | ||
|
|
||
| vg index -t ~{nb_cores} -j "~{output_prefix}.dist" ~{in_gbz_file} | ||
| } | ||
|
|
||
| output { | ||
| File output_dist_index = "~{output_prefix}.dist" | ||
| } | ||
| runtime { | ||
| preemptible: 2 | ||
| cpu: nb_cores | ||
| memory: in_extract_mem + " GB" | ||
| disks: "local-disk " + in_extract_disk + " SSD" | ||
| docker: "quay.io/vgteam/vg:v1.50.1" | ||
|
|
||
| } | ||
| } | ||
|
|
||
| task createRIndex { | ||
| input { | ||
| File in_gbz_file | ||
| Int nb_cores = 16 | ||
| Int in_extract_mem = 120 | ||
| Int in_extract_disk = 2 * round(size(in_gbz_file, "G")) + 20 | ||
| } | ||
|
|
||
| String out_prefix_name = sub( basename(in_gbz_file), "\\.gbz$", "") | ||
|
|
||
| command { | ||
| # Set the exit code of a pipeline to that of the rightmost command | ||
| # to exit with a non-zero status, or zero if all commands of the pipeline exit | ||
| set -o pipefail | ||
| # cause a bash script to exit immediately when a command fails | ||
| set -e | ||
| # cause the bash shell to treat unset variables as an error and exit immediately | ||
| set -u | ||
| # echo each line of the script to stdout so we can see what is happening | ||
| set -o xtrace | ||
| #to turn off echo do 'set +o xtrace' | ||
|
|
||
| vg gbwt -p --num-threads ~{nb_cores} -r ~{out_prefix_name}.ri -Z ~{in_gbz_file} | ||
|
|
||
| } | ||
|
|
||
| output { | ||
| File output_R_index = "~{out_prefix_name}.ri" | ||
| } | ||
| runtime { | ||
| preemptible: 2 | ||
| cpu: nb_cores | ||
| memory: in_extract_mem + " GB" | ||
| disks: "local-disk " + in_extract_disk + " SSD" | ||
| docker: "quay.io/vgteam/vg:v1.50.1" | ||
|
|
||
| } | ||
|
|
||
| } | ||
|
|
||
| task createHaplotypeIndex { | ||
| input { | ||
| File in_gbz_file | ||
| File in_dist_index | ||
| File in_R_index | ||
| Int kmer_length | ||
| Int window_length | ||
| Int subchain_length | ||
| Int nb_cores = 16 | ||
| Int in_extract_mem = 120 | ||
| Int in_extract_disk = 2 * round(size(in_gbz_file, "G") + size(in_dist_index, "G") + size(in_R_index, "G")) + 20 | ||
| } | ||
|
|
||
| String out_prefix_name = sub( basename(in_gbz_file), "\\.gbz$", "") | ||
|
|
||
| command { | ||
| # Set the exit code of a pipeline to that of the rightmost command | ||
| # to exit with a non-zero status, or zero if all commands of the pipeline exit | ||
| set -o pipefail | ||
| # cause a bash script to exit immediately when a command fails | ||
| set -e | ||
| # cause the bash shell to treat unset variables as an error and exit immediately | ||
| set -u | ||
| # echo each line of the script to stdout so we can see what is happening | ||
| set -o xtrace | ||
| #to turn off echo do 'set +o xtrace' | ||
|
|
||
|
|
||
| vg haplotypes -v 2 --kmer-length ~{kmer_length} \ | ||
| --window-length ~{window_length} \ | ||
| --subchain-length ~{subchain_length} \ | ||
| -t ~{nb_cores} -d ~{in_dist_index} \ | ||
| -r ~{in_R_index} -H ~{out_prefix_name}.hapl ~{in_gbz_file} | ||
|
|
||
| } | ||
|
|
||
| output { | ||
| File output_hap_index = "~{out_prefix_name}.hapl" | ||
| } | ||
| runtime { | ||
| preemptible: 2 | ||
| cpu: nb_cores | ||
| memory: in_extract_mem + " GB" | ||
| disks: "local-disk " + in_extract_disk + " SSD" | ||
| docker: "quay.io/vgteam/vg:v1.50.1" | ||
|
|
||
| } | ||
|
|
||
| } | ||
|
|
||
|
|
||
| task createMinimizerIndex { | ||
| input { | ||
| File in_gbz_file | ||
| File in_dist_index | ||
| String out_name | ||
| Int nb_cores = 16 | ||
| Int in_extract_mem = 120 | ||
| Int in_extract_disk = 4 * round(size(in_gbz_file, "G") + size(in_dist_index, "G")) + 20 | ||
| } | ||
|
|
||
| command { | ||
| # Set the exit code of a pipeline to that of the rightmost command | ||
| # to exit with a non-zero status, or zero if all commands of the pipeline exit | ||
| set -o pipefail | ||
| # cause a bash script to exit immediately when a command fails | ||
| set -e | ||
| # cause the bash shell to treat unset variables as an error and exit immediately | ||
| set -u | ||
| # echo each line of the script to stdout so we can see what is happening | ||
| set -o xtrace | ||
| #to turn off echo do 'set +o xtrace' | ||
|
|
||
| vg minimizer -p -t ~{nb_cores} -o ~{out_name}.min -d ~{in_dist_index} ~{in_gbz_file} | ||
|
|
||
| } | ||
|
|
||
| output { | ||
| File output_minimizer = "~{out_name}.min" | ||
| } | ||
| runtime { | ||
| preemptible: 2 | ||
| cpu: nb_cores | ||
| memory: in_extract_mem + " GB" | ||
| disks: "local-disk " + in_extract_disk + " SSD" | ||
| docker: "quay.io/vgteam/vg:v1.50.1" | ||
|
|
||
| } | ||
|
|
||
| } | ||
|
|
Oops, something went wrong.