From ab36f371f7732b8276b56ace20b6676192617362 Mon Sep 17 00:00:00 2001 From: dennishendriksen Date: Thu, 13 Jul 2023 08:33:52 +0200 Subject: [PATCH 1/3] bump vcf-report to 5.5.1 --- config/nxf.config | 2 +- config/nxf_vcf.config | 2 +- install.sh | 2 +- utils/apptainer/build.sh | 2 +- .../def/{vcf-report-5.5.0.def => vcf-report-5.5.1.def} | 4 ++-- 5 files changed, 6 insertions(+), 6 deletions(-) rename utils/apptainer/def/{vcf-report-5.5.0.def => vcf-report-5.5.1.def} (81%) diff --git a/config/nxf.config b/config/nxf.config index c5e6aece8..31a8b0be5 100644 --- a/config/nxf.config +++ b/config/nxf.config @@ -1,5 +1,5 @@ env { - VIP_VERSION = "5.7.2" + VIP_VERSION = "5.8.0" TMPDIR = "\${TMPDIR:-\${NXF_TEMP:-\$(mktemp -d)}}" APPTAINER_BIND = "${APPTAINER_BIND}" diff --git a/config/nxf_vcf.config b/config/nxf_vcf.config index e5d7988dc..7fd4f570f 100644 --- a/config/nxf_vcf.config +++ b/config/nxf_vcf.config @@ -11,7 +11,7 @@ env { CMD_FILTERVEP = "apptainer exec --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vep-109.3.sif filter_vep" CMD_BGZIP = "apptainer exec --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vep-109.3.sif bgzip" CMD_SAMTOOLS= "apptainer exec --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/samtools-1.17-patch1.sif samtools" - CMD_VCFREPORT="apptainer exec --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-report-5.5.0.sif" + CMD_VCFREPORT="apptainer exec --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-report-5.5.1.sif" CMD_VCFDECISIONTREE = "apptainer exec --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-decision-tree-3.5.4.sif" CMD_VCFINHERITANCEMATCHER = "apptainer exec --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-inheritance-matcher-2.1.6.sif" diff --git a/install.sh b/install.sh index 36fca4eb9..001fb9f8f 100755 --- a/install.sh +++ b/install.sh @@ -222,7 +222,7 @@ download_images() { files+=("samtools-1.17-patch1.sif") files+=("vcf-decision-tree-3.5.4.sif") files+=("vcf-inheritance-matcher-2.1.6.sif") - files+=("vcf-report-5.5.0.sif") + files+=("vcf-report-5.5.1.sif") files+=("vep-109.3.sif") files+=("manta-1.6.0.sif") files+=("gado-1.0.1.sif") diff --git a/utils/apptainer/build.sh b/utils/apptainer/build.sh index b4d9e4899..588bf8f5e 100644 --- a/utils/apptainer/build.sh +++ b/utils/apptainer/build.sh @@ -91,7 +91,7 @@ main() { images+=("samtools-1.17-patch1") images+=("vcf-decision-tree-3.5.4") images+=("vcf-inheritance-matcher-2.1.6") - images+=("vcf-report-5.5.0") + images+=("vcf-report-5.5.1") images+=("manta-1.6.0") for i in "${!images[@]}"; do diff --git a/utils/apptainer/def/vcf-report-5.5.0.def b/utils/apptainer/def/vcf-report-5.5.1.def similarity index 81% rename from utils/apptainer/def/vcf-report-5.5.0.def rename to utils/apptainer/def/vcf-report-5.5.1.def index 3aa3b2543..3a0b4e1c0 100644 --- a/utils/apptainer/def/vcf-report-5.5.0.def +++ b/utils/apptainer/def/vcf-report-5.5.1.def @@ -8,7 +8,7 @@ From: sif/build/openjdk-17.sif %post version_major=5 version_minor=5 - version_patch=0 + version_patch=1 # install apk update @@ -16,7 +16,7 @@ From: sif/build/openjdk-17.sif mkdir -p /opt/vcf-report/lib curl -Ls -o /opt/vcf-report/lib/vcf-report.jar "https://github.com/molgenis/vip-report/releases/download/v${version_major}.${version_minor}.${version_patch}/vcf-report.jar" - echo "71b3651e1b8ca5e0bb6ba2dd1349bfbf5867080690f0f53bdb1cc465f3781d76 /opt/vcf-report/lib/vcf-report.jar" | sha256sum -c + echo "791302158bf4b87faf6415011afb62efcd2225f42c635e7fd05bc8181fb3bead /opt/vcf-report/lib/vcf-report.jar" | sha256sum -c # cleanup apk del .build-dependencies From ff238ba5b9abdecc011b12c5705bc76d92534a31 Mon Sep 17 00:00:00 2001 From: dennishendriksen Date: Thu, 13 Jul 2023 08:40:45 +0200 Subject: [PATCH 2/3] update project_id param documentation --- docs/usage/input.md | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/docs/usage/input.md b/docs/usage/input.md index 9402c84e1..e033fd932 100644 --- a/docs/usage/input.md +++ b/docs/usage/input.md @@ -23,19 +23,19 @@ Sample-sheet values are case sensitive. Columns can contain values of different The following sections describe the columns that can be used in every sample-sheet followed by [workflow](workflow.md) specific columns. ## Columns -| column | type | required | default | description | -|-----------------------|-----------------|----------|-------------------------|-----------------------------------------| -| ``project_id`` | ``string`` | | ``vip`` | project identifier | -| ``family_id`` | ``string`` | | ``vip_fam`` | family identifier | -| ``individual_id`` | ``string`` | yes | | sample identifier of the individual | -| ``paternal_id`` | ``string`` | | | sample identifier of the father | -| ``maternal_id`` | ``string`` | | | sample identifier of the mother | -| ``sex`` | ``enum`` | | unknown sex | ``values: [male,female]`` | -| ``affected`` | ``boolean`` | | unknown affected status | whether the individual is affected | -| ``proband`` | ``boolean`` | | depends1 | individual being reported on | -| ``hpo_ids`` | ``string list`` | | | regex: `/HP:\d{7}/` | -| ``assembly`` | ``enum`` | | ``GRCh38`` | allowed values: [``GRCh37``,``GRCh38``] | -| ``sequencing_method`` | ``enum`` | | ``WGS`` | allowed values: [``WES``,``WGS``] | +| column | type | required | default | description | +|-----------------------|-----------------|----------|-------------------------|--------------------------------------------------------------| +| ``project_id`` | ``string`` | | ``vip`` | project identifier, see [here](../examples/multi-project.md) | +| ``family_id`` | ``string`` | | ``vip_fam`` | family identifier | +| ``individual_id`` | ``string`` | yes | | sample identifier of the individual | +| ``paternal_id`` | ``string`` | | | sample identifier of the father | +| ``maternal_id`` | ``string`` | | | sample identifier of the mother | +| ``sex`` | ``enum`` | | unknown sex | ``values: [male,female]`` | +| ``affected`` | ``boolean`` | | unknown affected status | whether the individual is affected | +| ``proband`` | ``boolean`` | | depends1 | individual being reported on | +| ``hpo_ids`` | ``string list`` | | | regex: `/HP:\d{7}/` | +| ``assembly`` | ``enum`` | | ``GRCh38`` | allowed values: [``GRCh37``,``GRCh38``] | +| ``sequencing_method`` | ``enum`` | | ``WGS`` | allowed values: [``WES``,``WGS``] | 1 Exception: if no probands are defined in the sample-sheet then all samples are considered to be probands. From 0bef83fae22701aef2de4e78f650dc79a94e0f7d Mon Sep 17 00:00:00 2001 From: dennishendriksen Date: Thu, 13 Jul 2023 08:41:52 +0200 Subject: [PATCH 3/3] resolve input.md formatting warning --- docs/usage/input.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/usage/input.md b/docs/usage/input.md index e033fd932..810cb724d 100644 --- a/docs/usage/input.md +++ b/docs/usage/input.md @@ -45,15 +45,15 @@ The following sections describe the columns that can be used in every sample-she | ``fastq`` | ``file list`` | yes2 | | allowed file extensions: [``fastq``, ``fastq.gz``, ``fq``, ``fq.gz``]. single-reads file(s) | | ``fastq_r1`` | ``file list`` | yes2 | | allowed file extensions: [``fastq``, ``fastq.gz``, ``fq``, ``fq.gz``]. paired-end reads file(s) #1 | | ``fastq_r2`` | ``file list`` | yes2 | | allowed file extensions: [``fastq``, ``fastq.gz``, ``fq``, ``fq.gz``]. paired-end reads file(s) #2 | -| ``sequencing_platform`` | ``enum`` | | ``illumina`` | allowed values: [``illumina``,``nanopore``,``pacbio_hifi``] | +| ``sequencing_platform`` | ``enum`` | | ``illumina`` | allowed values: [``illumina``,``nanopore``,``pacbio_hifi``] | 2 Either the `fastq` or the ``fastq_r1`` and ``fastq_r2`` are required. ## Columns: CRAM -| column | type | required | default | description | -|-------------------------|----------|----------|--------------|----------------------------------------------| -| ``cram`` | ``file`` | yes | | allowed file extensions: [``bam``, ``cram``] | -| ``sequencing_platform`` | ``enum`` | | ``illumina`` | allowed values: [``illumina``,``nanopore``,``pacbio_hifi``] | +| column | type | required | default | description | +|-------------------------|----------|----------|--------------|-------------------------------------------------------------| +| ``cram`` | ``file`` | yes | | allowed file extensions: [``bam``, ``cram``] | +| ``sequencing_platform`` | ``enum`` | | ``illumina`` | allowed values: [``illumina``,``nanopore``,``pacbio_hifi``] | ## Columns: VCF | column | type | required | default | description |