Develop

README.md

@@ -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) |

workflows/assemble_genome/assemble_genome.wdl

@@ -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 | \

workflows/de_novo_assembly_sample/de_novo_assembly_sample.wdl

@@ -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

workflows/main.wdl

@@ -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'"}