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paftools print version and minor doc fixes before merge
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@gconcepcion
gconcepcion committed Nov 28, 2023
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18 changes: 9 additions & 9 deletions README.md
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Expand Up @@ -191,13 +191,13 @@ The Docker image used by a particular step of the workflow can be identified by
| Image | Major tool versions | Links |
| :- | :- | :- |
| align_hifiasm | <ul><li>[minimap2 2.17](https://github.com/lh3/minimap2/releases/tag/v2.17)</li><li>[samtools 1.14](https://github.com/samtools/samtools/releases/tag/1.14)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/987efde4d614a292fbfe9f3cf146b63005ad6a8a/docker/align_hifiasm) |
| bcftools | <ul><li>[bcftools 1.14](https://github.com/samtools/bcftools/releases/tag/1.14)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/987efde4d614a292fbfe9f3cf146b63005ad6a8a/docker/bcftools) |
| gfatools | <ul><li>[gfatools 0.4](https://github.com/lh3/gfatools/releases/tag/v0.4)</li><li>[htslib 1.14](https://github.com/samtools/htslib/releases/tag/1.14)</li><li>[k8 0.2.5](https://github.com/attractivechaos/k8/releases/tag/0.2.5)</li><li>[caln50 01091f2](https://github.com/lh3/calN50/tree/01091f25bc24e17fbf0da3407ea24aa448c489ae)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/987efde4d614a292fbfe9f3cf146b63005ad6a8a/docker/gfatools) |
| hifiasm | <ul><li>[hifiasm 0.19.4](https://github.com/chhylp123/hifiasm/releases/tag/0.19.4)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/987efde4d614a292fbfe9f3cf146b63005ad6a8a/docker/hifiasm) |
| htslib | <ul><li>[htslib 1.14](https://github.com/samtools/htslib/releases/tag/1.14)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/987efde4d614a292fbfe9f3cf146b63005ad6a8a/docker/htslib) |
| paftools | <ul><li>[minimap2 2.17](https://github.com/lh3/minimap2/releases/tag/v2.17)</li><li>[samtools 1.14](https://github.com/samtools/samtools/releases/tag/1.14)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/987efde4d614a292fbfe9f3cf146b63005ad6a8a/docker/align_hifiasm) |
| align_hifiasm | <ul><li>[minimap2 2.17](https://github.com/lh3/minimap2/releases/tag/v2.17)</li><li>[samtools 1.14](https://github.com/samtools/samtools/releases/tag/1.14)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/align_hifiasm) |
| bcftools | <ul><li>[bcftools 1.14](https://github.com/samtools/bcftools/releases/tag/1.14)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/bcftools) |
| gfatools | <ul><li>[gfatools 0.4](https://github.com/lh3/gfatools/releases/tag/v0.4)</li><li>[htslib 1.14](https://github.com/samtools/htslib/releases/tag/1.14)</li><li>[k8 0.2.5](https://github.com/attractivechaos/k8/releases/tag/0.2.5)</li><li>[caln50 01091f2](https://github.com/lh3/calN50/tree/01091f25bc24e17fbf0da3407ea24aa448c489ae)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/gfatools) |
| hifiasm | <ul><li>[hifiasm 0.19.4](https://github.com/chhylp123/hifiasm/releases/tag/0.19.4)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/hifiasm) |
| htslib | <ul><li>[htslib 1.14](https://github.com/samtools/htslib/releases/tag/1.14)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/htslib) |
| paftools | <ul<li>[paftools 2.26-r1182-dirty](https://github.com/lh3/minimap2/blob/bc588c0eeb26426d0d90a93fb0877358a389c515/misc/paftools.js)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/align_hifiasm) |
| parse-cohort | <ul><li>python 3.8.10; custom scripts</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/
987efde4d614a292fbfe9f3cf146b63005ad6a8a/docker/parse-cohort) |
| samtools | <ul><li>[samtools 1.14](https://github.com/samtools/samtools/releases/tag/1.14)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/987efde4d614a292fbfe9f3cf146b63005ad6a8a/docker/samtools) |
| yak | <ul><li>[yak 0.1](https://github.com/lh3/yak/releases/tag/v0.1)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/987efde4d614a292fbfe9f3cf146b63005ad6a8a/docker/yak) |
3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/parse-cohort) |
| samtools | <ul><li>[samtools 1.14](https://github.com/samtools/samtools/releases/tag/1.14)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/samtools) |
| yak | <ul><li>[yak 0.1](https://github.com/lh3/yak/releases/tag/v0.1)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/yak) |
2 changes: 2 additions & 0 deletions workflows/assemble_genome/assemble_genome.wdl
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Expand Up @@ -342,6 +342,8 @@ task paftools {
command <<<
set -euo pipefail
k8 /opt/minimap2-2.17/misc/paftools.js version
samtools view -h ~{bam} | \
k8 /opt/minimap2-2.17/misc/paftools.js sam2paf - | \
sort -k6,6 -k8,8n | \
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1 change: 0 additions & 1 deletion workflows/de_novo_assembly_sample/de_novo_assembly_sample.wdl
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Expand Up @@ -79,7 +79,6 @@ workflow de_novo_assembly_sample {
Array[File] zipped_assembly_fastas = assemble_genome.zipped_assembly_fastas
Array[File] assembly_stats = assemble_genome.assembly_stats
Array[IndexData] merged_bams = assemble_genome.merged_bams
#Array[IndexData] asm_bams = assemble_genome.asm_bams

Array[IndexData] paftools_vcfs = paftools_vcf
Array[File] paftools_vcf_stats = bcftools_stats.stats
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4 changes: 2 additions & 2 deletions workflows/main.wdl
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Expand Up @@ -86,8 +86,8 @@ workflow de_novo_assembly {

parameter_meta {
cohort: {help: "Sample information for the cohort"}
reference: {help: "Reference genome data"}
backend: {help: "Backend where the workflow will be executed ['GCP', 'Azure', 'AWS']"}
reference: {help: "Array of Reference genome data"}
backend: {help: "Backend where the workflow will be executed ['GCP', 'Azure', 'AWS', 'HPC']"}
zones: {help: "Zones where compute will take place; required if backend is set to 'AWS' or 'GCP'"}
aws_spot_queue_arn: {help: "Queue ARN for the spot batch queue; required if backend is set to 'AWS'"}
aws_on_demand_queue_arn: {help: "Queue ARN for the on demand batch queue; required if backend is set to 'AWS'"}
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