Build branch main with version main (0c8a7eb)
Build pipeline: viash-hub.rnaseq.main-nn8dl
Source commit: 0c8a7eb648
Source message: remove citation
This commit is contained in:
@@ -1,268 +0,0 @@
|
||||
name: "bbmap_bbsplit"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--id"
|
||||
description: "Sample ID"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--paired"
|
||||
description: "Paired fastq files or not?"
|
||||
info: null
|
||||
default:
|
||||
- false
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "Input fastq files, either one or two (paired)"
|
||||
info: null
|
||||
example:
|
||||
- "sample.fastq"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ","
|
||||
- type: "file"
|
||||
name: "--primary_ref"
|
||||
description: "Primary reference FASTA"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--bbsplit_fasta_list"
|
||||
description: "Path to comma-separated file containing a list of reference genomes\
|
||||
\ to filter reads against with BBSplit."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--only_build_index"
|
||||
description: "true = only build index; false = mapping"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--built_bbsplit_index"
|
||||
description: "Directory with index files"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--fastq_1"
|
||||
description: "Output file for read 1."
|
||||
info: null
|
||||
default:
|
||||
- "$id.$key.read_1.fastq"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--fastq_2"
|
||||
description: "Output file for read 2."
|
||||
info: null
|
||||
default:
|
||||
- "$id.$key.read_2.fastq"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--bbsplit_index"
|
||||
description: "Directory with index files"
|
||||
info: null
|
||||
default:
|
||||
- "BBSplit_index"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Split sequencing reads by mapping them to multiple references simultaneously.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "genome.fasta"
|
||||
- type: "file"
|
||||
path: "SRR6357070_1.fastq.gz"
|
||||
- type: "file"
|
||||
path: "SRR6357070_2.fastq.gz"
|
||||
- type: "file"
|
||||
path: "sarscov2.fa"
|
||||
- type: "file"
|
||||
path: "human.fa"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/bbmap/bbsplit/main.nf"
|
||||
- "modules/nf-core/bbmap/bbsplit/meta.yml"
|
||||
last_sha: "277bd337739a8b8f753fa7b5eda6743b9b6acb89"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "docker"
|
||||
run:
|
||||
- "apt-get update && \\\napt-get install -y build-essential openjdk-17-jdk wget\
|
||||
\ tar && \\\nwget --no-check-certificate https://sourceforge.net/projects/bbmap/files/BBMap_39.01.tar.gz\
|
||||
\ && \\\ntar xzf BBMap_39.01.tar.gz && \\\ncp -r bbmap/* /usr/local/bin\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/bbmap_bbsplit/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/bbmap_bbsplit"
|
||||
executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -83,7 +83,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -178,8 +178,8 @@ build_info:
|
||||
output: "target/executable/bedtools_genomecov"
|
||||
executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -190,7 +190,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \
|
||||
chmod a+x /usr/local/bin/bedtools
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:29Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:51Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -93,7 +93,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -182,8 +182,8 @@ build_info:
|
||||
output: "target/executable/cat_additional_fasta"
|
||||
executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -194,7 +194,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -480,9 +480,9 @@ function ViashDockerfile {
|
||||
FROM python:latest
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:28Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:50Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -80,7 +80,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -169,8 +169,8 @@ build_info:
|
||||
output: "target/executable/cat_fastq"
|
||||
executable: "target/executable/cat_fastq/cat_fastq"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -181,7 +181,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -472,9 +472,9 @@ function ViashDockerfile {
|
||||
FROM ubuntu:22.04
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.description="Companion container for running component cat_fastq"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:27Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:49Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -136,7 +136,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -237,8 +237,8 @@ build_info:
|
||||
output: "target/executable/deseq2_qc"
|
||||
executable: "target/executable/deseq2_qc/deseq2_qc"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -249,7 +249,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -506,9 +506,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
|
||||
Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr", "matrixStats"), repos = "https://cran.rstudio.com")'
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:30Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:49Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -168,7 +168,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -266,8 +266,8 @@ build_info:
|
||||
output: "target/executable/dupradar"
|
||||
executable: "target/executable/dupradar/dupradar"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -278,7 +278,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -520,9 +520,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
|
||||
Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")'
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component dupradar"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:30Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:51Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -1,228 +0,0 @@
|
||||
name: "fastqc"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "boolean"
|
||||
name: "--paired"
|
||||
description: "Paired fastq files or not?"
|
||||
info: null
|
||||
default:
|
||||
- false
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "Input fastq files, either one or two (paired)"
|
||||
info: null
|
||||
example:
|
||||
- "sample.fastq"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ","
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--fastqc_html_1"
|
||||
description: "FastQC HTML report for read 1."
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_1.fastqc.html"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--fastqc_html_2"
|
||||
description: "FastQC HTML report for read 2."
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_2.fastqc.html"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--fastqc_zip_1"
|
||||
description: "FastQC report archive for read 1."
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_1.fastqc.zip"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--fastqc_zip_2"
|
||||
description: "FastQC report archive for read 2."
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_2.fastqc.zip"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Fastqc component, please see https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.\
|
||||
\ This component can take one or more files (by means of shell globbing) or a complete\
|
||||
\ directory.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "SRR6357070_1.fastq.gz"
|
||||
- type: "file"
|
||||
path: "SRR6357070_2.fastq.gz"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/fastqc/main.nf"
|
||||
- "modules/nf-core/fastqc/meta.yml"
|
||||
last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "fastqc"
|
||||
interactive: false
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/fastqc/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/fastqc"
|
||||
executable: "target/executable/fastqc/fastqc"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,207 +0,0 @@
|
||||
name: "fq_subsample"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "Input fastq files to subsample"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_args"
|
||||
description: "Extra arguments to pass to fq subsample"
|
||||
info: null
|
||||
default:
|
||||
- ""
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output_1"
|
||||
description: "Sampled read 1 fastq files"
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_1.subsampled.fastq"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_2"
|
||||
description: "Sampled read 2 fastq files"
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_2.subsampled.fastq"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "fq subsample outputs a subset of records from single or paired FASTQ\
|
||||
\ files. This requires a seed (--seed) to be set in ext.args\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "SRR6357070_1.fastq.gz"
|
||||
- type: "file"
|
||||
path: "SRR6357070_2.fastq.gz"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/fq/subsample/main.nf"
|
||||
- "modules/nf-core/fq/subsample/meta.yml"
|
||||
last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "docker"
|
||||
run:
|
||||
- "ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone\
|
||||
\ && \\\napt-get update && \\\napt-get install -y --no-install-recommends build-essential\
|
||||
\ git-all curl && \\\ncurl https://sh.rustup.rs -sSf | sh -s -- -y && \\\n.\
|
||||
\ \"$HOME/.cargo/env\" && \\\ngit clone --depth 1 --branch v0.12.0 https://github.com/stjude-rust-labs/fq.git\
|
||||
\ && \\\nmv fq /usr/local/ && cd /usr/local/fq && \\\ncargo install --locked\
|
||||
\ --path . && \\\nmv /usr/local/fq/target/release/fq /usr/local/bin/\n"
|
||||
env:
|
||||
- "TZ=Europe/Brussels"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/fq_subsample/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/fq_subsample"
|
||||
executable: "target/executable/fq_subsample/fq_subsample"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -70,7 +70,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -167,8 +167,8 @@ build_info:
|
||||
output: "target/executable/getchromsizes"
|
||||
executable: "target/executable/getchromsizes/getchromsizes"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -179,7 +179,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -480,9 +480,9 @@ make && \
|
||||
make install
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:29Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:50Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -51,7 +51,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -145,8 +145,8 @@ build_info:
|
||||
output: "target/executable/gtf2bed"
|
||||
executable: "target/executable/gtf2bed/gtf2bed"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -157,7 +157,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -466,9 +466,9 @@ RUN apt-get update && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component gtf2bed"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:30Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:51Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -66,7 +66,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -155,8 +155,8 @@ build_info:
|
||||
output: "target/executable/gtf_filter"
|
||||
executable: "target/executable/gtf_filter/gtf_filter"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -167,7 +167,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -470,9 +470,9 @@ function ViashDockerfile {
|
||||
FROM python:latest
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.description="Companion container for running component gtf_filter"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:29Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:50Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -50,7 +50,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -144,8 +144,8 @@ build_info:
|
||||
output: "target/executable/gunzip"
|
||||
executable: "target/executable/gunzip/gunzip"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -156,7 +156,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -466,9 +466,9 @@ RUN apt-get update && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component gunzip"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:24Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:46Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -1,185 +0,0 @@
|
||||
name: "kallisto_index"
|
||||
namespace: "kallisto"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--transcriptome_fasta"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--pseudo_aligner_kmer_size"
|
||||
description: "Kmer length passed to indexing step of pseudoaligners."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--kallisto_index"
|
||||
info: null
|
||||
default:
|
||||
- "Kallisto_index"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Create Kallisto index.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "transcriptome.fasta"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/kallisto/index/main.nf"
|
||||
- "modules/nf-core/kallisto/index/meta.yml"
|
||||
last_sha: "c0816976384d5e7ee6079c29c45958df1ffa0ee4"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "docker"
|
||||
run:
|
||||
- "apt-get update && \\\napt-get install -y --no-install-recommends wget && \\\
|
||||
\nwget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz\
|
||||
\ && \\\ntar -xzf kallisto_linux-v0.50.1.tar.gz && \\\nmv kallisto/kallisto\
|
||||
\ /usr/local/bin/\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/kallisto/kallisto_index/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/kallisto/kallisto_index"
|
||||
executable: "target/executable/kallisto/kallisto_index/kallisto_index"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,283 +0,0 @@
|
||||
name: "kallisto_quant"
|
||||
namespace: "kallisto"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "List of input FastQ files of size 1 and 2 for single-end and paired-end\
|
||||
\ data, respectively."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ","
|
||||
- type: "boolean"
|
||||
name: "--paired"
|
||||
description: "Paired reads or not."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--strandedness"
|
||||
description: "Sample strand-specificity."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--index"
|
||||
description: "Kallisto genome index."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--gtf"
|
||||
description: "Optional gtf file for translation of transcripts into genomic coordinates."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--chromosomes"
|
||||
description: "Optional tab separated file with chromosome names and lengths."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--fragment_length"
|
||||
description: "For single-end mode only, the estimated average fragment length."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--fragment_length_sd"
|
||||
description: "For single-end mode only, the estimated standard deviation of the\
|
||||
\ fragment length."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "Kallisto quant results"
|
||||
info: null
|
||||
default:
|
||||
- "$id.kallisto_quant_results"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--log"
|
||||
description: "File containing log information from running kallisto quant"
|
||||
info: null
|
||||
default:
|
||||
- "$id.kallisto_quant.log.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--run_info"
|
||||
description: "A json file containing information about the run"
|
||||
info: null
|
||||
default:
|
||||
- "$id.run_info.json"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--quant_results_file"
|
||||
description: "TSV file containing abundance estimates from Kallisto"
|
||||
info: null
|
||||
default:
|
||||
- "$id.abundance.tsv"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Computes equivalence classes for reads and quantifies abundances.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "transcriptome.fasta"
|
||||
- type: "file"
|
||||
path: "SRR6357070_1.fastq.gz"
|
||||
- type: "file"
|
||||
path: "SRR6357070_2.fastq.gz"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/kallisto/quant/main.nf"
|
||||
- "modules/nf-core/kallisto/quant/meta.yml"
|
||||
last_sha: "aff1d2e02717247831644769fc3ba84868c3fdde"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "docker"
|
||||
run:
|
||||
- "apt-get update && \\\napt-get install -y --no-install-recommends wget && \\\
|
||||
\nwget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz\
|
||||
\ && \\\ntar -xzf kallisto_linux-v0.50.1.tar.gz && \\\nmv kallisto/kallisto\
|
||||
\ /usr/local/bin/\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/kallisto/kallisto_quant/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/kallisto/kallisto_quant"
|
||||
executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -76,7 +76,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -165,8 +165,8 @@ build_info:
|
||||
output: "target/executable/multiqc_custom_biotype"
|
||||
executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -177,7 +177,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -476,9 +476,9 @@ function ViashDockerfile {
|
||||
FROM python:latest
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:28Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:49Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -110,7 +110,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -207,8 +207,8 @@ build_info:
|
||||
output: "target/executable/picard_markduplicates"
|
||||
executable: "target/executable/picard_markduplicates/picard_markduplicates"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -219,7 +219,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -494,9 +494,9 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do
|
||||
mv picard.jar /usr/local/bin
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:26Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:47Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -320,7 +320,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -409,8 +409,8 @@ build_info:
|
||||
output: "target/executable/prepare_multiqc_input"
|
||||
executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -421,7 +421,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -557,9 +557,9 @@ function ViashDockerfile {
|
||||
FROM ubuntu:22.04
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:22Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:46Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -49,7 +49,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -138,8 +138,8 @@ build_info:
|
||||
output: "target/executable/preprocess_transcripts_fasta"
|
||||
executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -150,7 +150,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -462,9 +462,9 @@ function ViashDockerfile {
|
||||
FROM ubuntu:22.04
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:27Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:47Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -70,7 +70,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -191,8 +191,8 @@ build_info:
|
||||
output: "target/executable/preseq_lcextrap"
|
||||
executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -203,7 +203,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -495,9 +495,9 @@ mkdir build && cd build && \
|
||||
make && make install && make HAVE_HTSLIB=1 all
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:26Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:47Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -1,301 +0,0 @@
|
||||
name: "qualimap"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "path to input mapping file in BAM format."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--gtf"
|
||||
description: "path to annotations file in Ensembl GTF format."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output_dir"
|
||||
description: "path to output directory for raw data and report."
|
||||
info: null
|
||||
default:
|
||||
- "$id.qualimap_output"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_pdf"
|
||||
description: "path to output file for pdf report."
|
||||
info: null
|
||||
default:
|
||||
- "$id.report.pdf"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_format"
|
||||
description: "Format of the output report (PDF or HTML, default is HTML)"
|
||||
info: null
|
||||
default:
|
||||
- "html"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Optional"
|
||||
arguments:
|
||||
- type: "integer"
|
||||
name: "--pr_bases"
|
||||
description: "Number of upstream/downstream nucleotide bases to compute 5'-3'\
|
||||
\ bias (default = 100)."
|
||||
info: null
|
||||
default:
|
||||
- 100
|
||||
required: false
|
||||
min: 1
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--tr_bias"
|
||||
description: "Number of top highly expressed transcripts to compute 5'-3' bias\
|
||||
\ (default = 1000)."
|
||||
info: null
|
||||
default:
|
||||
- 1000
|
||||
required: false
|
||||
min: 1
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--algorithm"
|
||||
description: "Counting algorithm (uniquely-mapped-reads (default) or proportional)."
|
||||
info: null
|
||||
default:
|
||||
- "uniquely-mapped-reads"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--sequencing_protocol"
|
||||
description: "Sequencing library protocol (strand-specific-forward, strand-specific-reverse\
|
||||
\ or non-strand-specific (default))."
|
||||
info: null
|
||||
default:
|
||||
- "non-strand-specific"
|
||||
required: false
|
||||
choices:
|
||||
- "non-strand-specific"
|
||||
- "strand-specific-reverse"
|
||||
- "strand-specific-forward"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--paired"
|
||||
description: "Setting this flag for paired-end experiments will result in counting\
|
||||
\ fragments instead of reads."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--sorted"
|
||||
description: "Setting this flag indicates that the input file is already sorted\
|
||||
\ by name. If flag is not set, additional sorting by name will be performed.\
|
||||
\ Only requiredfor paired-end analysis."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "string"
|
||||
name: "--java_memory_size"
|
||||
description: "maximum Java heap memory size, default = 4G."
|
||||
info: null
|
||||
default:
|
||||
- "4G"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "RNA-seq QC analysis using the qualimap \n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam"
|
||||
- type: "file"
|
||||
path: "wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam.bai"
|
||||
- type: "file"
|
||||
path: "genes.gtf"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/qualimap/rnaseq/main.nf"
|
||||
last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "r-base"
|
||||
- "unzip"
|
||||
- "wget"
|
||||
- "openjdk-8-jdk"
|
||||
- "libxml2-dev"
|
||||
- "libcurl4-openssl-dev"
|
||||
interactive: false
|
||||
- type: "docker"
|
||||
run:
|
||||
- "wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip &&\
|
||||
\ \\\nunzip qualimap_v2.3.zip && \\\ncp -a qualimap_v2.3/. usr/bin && \\\nunset\
|
||||
\ DISPLAY && \\\nmkdir -p tmp && \\\nexport _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp\n"
|
||||
- type: "r"
|
||||
cran:
|
||||
- "optparse"
|
||||
bioc:
|
||||
- "NOISeqr"
|
||||
bioc_force_install: false
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/qualimap/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/qualimap"
|
||||
executable: "target/executable/qualimap/qualimap"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,329 +0,0 @@
|
||||
name: "rsem_calculate_expression"
|
||||
namespace: "rsem"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--id"
|
||||
description: "Sample ID."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--strandedness"
|
||||
description: "Sample strand-specificity. Must be one of unstranded, forward, reverse"
|
||||
info: null
|
||||
required: false
|
||||
choices:
|
||||
- "forward"
|
||||
- "reverse"
|
||||
- "unstranded"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--paired"
|
||||
description: "Paired-end reads or not?"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "Input reads for quantification."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--index"
|
||||
description: "RSEM index."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_args"
|
||||
description: "Extra rsem-calculate-expression arguments in addition to the defaults."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--counts_gene"
|
||||
description: "Expression counts on gene level"
|
||||
info: null
|
||||
example:
|
||||
- "sample.genes.results"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--counts_transcripts"
|
||||
description: "Expression counts on transcript level"
|
||||
info: null
|
||||
example:
|
||||
- "sample.isoforms.results"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--stat"
|
||||
description: "RSEM statistics"
|
||||
info: null
|
||||
example:
|
||||
- "sample.stat"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--logs"
|
||||
description: "RSEM logs"
|
||||
info: null
|
||||
example:
|
||||
- "sample.log"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--bam_star"
|
||||
description: "BAM file generated by STAR (optional)"
|
||||
info: null
|
||||
example:
|
||||
- "sample.STAR.genome.bam"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--bam_genome"
|
||||
description: "Genome BAM file (optional)"
|
||||
info: null
|
||||
example:
|
||||
- "sample.genome.bam"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--bam_transcript"
|
||||
description: "Transcript BAM file (optional)"
|
||||
info: null
|
||||
example:
|
||||
- "sample.transcript.bam"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Calculate expression with RSEM.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "SRR6357070_1.fastq.gz"
|
||||
- type: "file"
|
||||
path: "SRR6357070_2.fastq.gz"
|
||||
- type: "file"
|
||||
path: "rsem.tar.gz"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/rsem/calculateexpression/main.nf"
|
||||
- "modules/nf-core/rsem/calculateexpression/meta.yml"
|
||||
last_sha: "92b2a7857de1dda9d1c19a088941fc81e2976ff7"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "build-essential"
|
||||
- "gcc"
|
||||
- "g++"
|
||||
- "make"
|
||||
- "wget"
|
||||
- "zlib1g-dev"
|
||||
- "unzip"
|
||||
- "xxd"
|
||||
- "perl"
|
||||
- "r-base"
|
||||
- "bowtie2"
|
||||
- "python3-pip"
|
||||
- "git"
|
||||
interactive: false
|
||||
- type: "docker"
|
||||
run:
|
||||
- "ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone\
|
||||
\ && \\\ncd /tmp && \\\nwget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/${STAR_VERSION}.zip\
|
||||
\ && \\\nunzip ${STAR_VERSION}.zip && \\\ncd STAR-${STAR_VERSION}/source &&\
|
||||
\ \\\nmake STARstatic CXXFLAGS_SIMD=-std=c++11 && \\\ncp STAR /usr/local/bin\
|
||||
\ && \\\ncd /tmp && \\\nwget --no-check-certificate https://github.com/deweylab/RSEM/archive/refs/tags/v${RSEM_VERSION}.zip\
|
||||
\ && \\\nunzip v${RSEM_VERSION}.zip && \\\ncd RSEM-${RSEM_VERSION} && \\\nmake\
|
||||
\ && \\\nmake install && \\\nrm -rf /tmp/STAR-${STAR_VERSION} /tmp/${STAR_VERSION}.zip\
|
||||
\ && \\\nrm -rf /tmp/RSEM-${RSEM_VERSION} /tmp/v${RSEM_VERSION}.zip && \\\n\
|
||||
cd && \\\napt-get clean && \\\necho 'export PATH=$PATH:/usr/local/bin' >> /etc/profile\
|
||||
\ && \\\necho 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \\\n/bin/bash\
|
||||
\ -c \"source /etc/profile && source ~/.bashrc && echo $PATH && which STAR\"\
|
||||
\n"
|
||||
env:
|
||||
- "STAR_VERSION=2.7.11b"
|
||||
- "RSEM_VERSION=1.3.3"
|
||||
- "TZ=Europe/Brussels"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/rsem/rsem_calculate_expression/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/rsem/rsem_calculate_expression"
|
||||
executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,5 +1,4 @@
|
||||
name: "rsem_merge_counts"
|
||||
namespace: "rsem"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
@@ -93,7 +92,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -176,14 +175,14 @@ engines:
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/rsem/rsem_merge_counts/config.vsh.yaml"
|
||||
config: "src/rsem_merge_counts/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/rsem/rsem_merge_counts"
|
||||
executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts"
|
||||
output: "target/executable/rsem_merge_counts"
|
||||
executable: "target/executable/rsem_merge_counts/rsem_merge_counts"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -194,7 +193,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -482,10 +482,10 @@ function ViashDockerfile {
|
||||
cat << 'VIASHDOCKER'
|
||||
FROM ubuntu:22.04
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:23Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rsem_merge_counts"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:49Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
@@ -779,7 +779,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
||||
|
||||
# determine docker image id
|
||||
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
|
||||
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rsem/rsem_merge_counts:main'
|
||||
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rsem_merge_counts:main'
|
||||
fi
|
||||
|
||||
# print dockerfile
|
||||
@@ -1,193 +0,0 @@
|
||||
name: "rseqc_bamstat"
|
||||
namespace: "rseqc"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "input alignment file in BAM or SAM format"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--map_qual"
|
||||
description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
|
||||
\ reads, default=30."
|
||||
info: null
|
||||
default:
|
||||
- 30
|
||||
required: false
|
||||
min: 0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "output file (txt) with mapping quality statistics"
|
||||
info: null
|
||||
default:
|
||||
- "$id.mapping_quality.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Generate statistics from a bam file.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test.paired_end.sorted.bam"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/rseqc/bamstat/main.nf"
|
||||
last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "python3-pip"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "RSeQC"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/rseqc/rseqc_bamstat/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/rseqc/rseqc_bamstat"
|
||||
executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,216 +0,0 @@
|
||||
name: "rseqc_inferexperiment"
|
||||
namespace: "rseqc"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "input alignment file in BAM or SAM format"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--refgene"
|
||||
description: "Reference gene model in bed format"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--sample_size"
|
||||
description: "Numer of reads sampled from SAM/BAM file, default = 200000."
|
||||
info: null
|
||||
default:
|
||||
- 200000
|
||||
required: false
|
||||
min: 1
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--map_qual"
|
||||
description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
|
||||
\ reads, default=30."
|
||||
info: null
|
||||
default:
|
||||
- 30
|
||||
required: false
|
||||
min: 0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "output file (txt) of strandness report"
|
||||
info: null
|
||||
default:
|
||||
- "$id.strandedness.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Infer strandedness from sequencing reads\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test.paired_end.sorted.bam"
|
||||
- type: "file"
|
||||
path: "test.bed12"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/rseqc/inferexperiment/main.nf"
|
||||
last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "python3-pip"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "RSeQC"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/rseqc/rseqc_inferexperiment/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/rseqc/rseqc_inferexperiment"
|
||||
executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,302 +0,0 @@
|
||||
name: "rseqc_innerdistance"
|
||||
namespace: "rseqc"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "input alignment file in BAM or SAM format"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--refgene"
|
||||
description: "Reference gene model in bed format"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--sample_size"
|
||||
description: "Numer of reads sampled from SAM/BAM file, default = 200000."
|
||||
info: null
|
||||
default:
|
||||
- 200000
|
||||
required: false
|
||||
min: 1
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--map_qual"
|
||||
description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
|
||||
\ reads, default=30."
|
||||
info: null
|
||||
default:
|
||||
- 30
|
||||
required: false
|
||||
min: 0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--lower_bound_size"
|
||||
description: "Lower bound of inner distance (bp). This option is used for ploting\
|
||||
\ histograme, default=-250."
|
||||
info: null
|
||||
default:
|
||||
- -250
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--upper_bound_size"
|
||||
description: "Upper bound of inner distance (bp). This option is used for ploting\
|
||||
\ histograme, default=250."
|
||||
info: null
|
||||
default:
|
||||
- 250
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--step_size"
|
||||
description: "Step size (bp) of histograme. This option is used for plotting histogram,\
|
||||
\ default=5."
|
||||
info: null
|
||||
default:
|
||||
- 5
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output_stats"
|
||||
description: "output file (txt) with summary statistics of inner distances of\
|
||||
\ paired reads"
|
||||
info: null
|
||||
default:
|
||||
- "$id.inner_distance.stats"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_dist"
|
||||
description: "output file (txt) with inner distances of all paired reads"
|
||||
info: null
|
||||
default:
|
||||
- "$id.inner_distance.txt"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_freq"
|
||||
description: "output file (txt) with frequencies of inner distances of all paired\
|
||||
\ reads"
|
||||
info: null
|
||||
default:
|
||||
- "$id.inner_distance_freq.txt"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_plot"
|
||||
description: "output file (pdf) with histogram plot of of inner distances of all\
|
||||
\ paired reads"
|
||||
info: null
|
||||
default:
|
||||
- "$id.inner_distance_plot.pdf"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_plot_r"
|
||||
description: "output file (R) with script of histogram plot of of inner distances\
|
||||
\ of all paired reads"
|
||||
info: null
|
||||
default:
|
||||
- "$id.inner_distance_plot.r"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Calculate inner distance between read pairs. \n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test.paired_end.sorted.bam"
|
||||
- type: "file"
|
||||
path: "test.bed12"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/rseqc/innerdistance/main.nf"
|
||||
last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "python3-pip"
|
||||
- "r-base"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "RSeQC"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/rseqc/rseqc_innerdistance/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/rseqc/rseqc_innerdistance"
|
||||
executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -160,7 +160,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -260,8 +260,8 @@ build_info:
|
||||
output: "target/executable/rseqc/rseqc_junctionannotation"
|
||||
executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -272,7 +272,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -519,9 +519,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "RSeQC"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:28Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:48Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -149,7 +149,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -249,8 +249,8 @@ build_info:
|
||||
output: "target/executable/rseqc/rseqc_junctionsaturation"
|
||||
executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -261,7 +261,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -522,9 +522,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "RSeQC"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:29Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:49Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -63,7 +63,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -162,8 +162,8 @@ build_info:
|
||||
output: "target/executable/rseqc/rseqc_readdistribution"
|
||||
executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -174,7 +174,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -474,9 +474,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "RSeQC"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:29Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:49Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -111,7 +111,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -211,8 +211,8 @@ build_info:
|
||||
output: "target/executable/rseqc/rseqc_readduplication"
|
||||
executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -223,7 +223,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -499,9 +499,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "RSeQC"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:27Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:48Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -117,7 +117,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -214,8 +214,8 @@ build_info:
|
||||
output: "target/executable/rseqc/rseqc_tin"
|
||||
executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -226,7 +226,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -501,9 +501,9 @@ RUN apt-get update && \
|
||||
RUN pip3 install RSeQC
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:29Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:48Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -103,7 +103,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -192,8 +192,8 @@ build_info:
|
||||
output: "target/executable/sortmerna"
|
||||
executable: "target/executable/sortmerna/sortmerna"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -204,7 +204,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -486,9 +486,9 @@ function ViashDockerfile {
|
||||
FROM quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:32Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:52Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -120,7 +120,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -216,8 +216,8 @@ build_info:
|
||||
output: "target/executable/stringtie"
|
||||
executable: "target/executable/stringtie/stringtie"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -228,7 +228,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -496,9 +496,9 @@ tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \
|
||||
cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component stringtie"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:33Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:52Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -99,7 +99,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -199,8 +199,8 @@ build_info:
|
||||
output: "target/executable/summarizedexperiment"
|
||||
executable: "target/executable/summarizedexperiment/summarizedexperiment"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -211,7 +211,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -487,9 +487,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
|
||||
Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")'
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:31Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:52Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -1,818 +0,0 @@
|
||||
name: "trimgalore"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "Input files. Note that paired-end files need to be supplied in a\
|
||||
\ pairwise fashion, e.g. file1_1.fq file1_2.fq SRR2_1.fq.gz SRR2_2.fq.gz"
|
||||
info: null
|
||||
example:
|
||||
- "sample1_r1.fq;sample1_r2.fq;sample2_r1.fq;sample2_r2.fq"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- name: "Trimming options"
|
||||
arguments:
|
||||
- type: "integer"
|
||||
name: "--quality"
|
||||
alternatives:
|
||||
- "-q"
|
||||
description: "Trim low-quality ends (below the specified Phred score) from reads\
|
||||
\ in addition to adapter removal. For RRBS samples, quality trimming will be\
|
||||
\ performed first, and adapter trimming is carried in a second round. Other\
|
||||
\ files are quality and adapter trimmed in a single pass. The algorithm is the\
|
||||
\ same as the one used by BWA (Subtract INT from all qualities; compute partial\
|
||||
\ sums from all indices to the end of the sequence; cut sequence at the index\
|
||||
\ at which the sum is minimal)."
|
||||
info: null
|
||||
example:
|
||||
- 20
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--phred33"
|
||||
description: "Instructs Cutadapt to use ASCII+33 quality scores as Phred scores\
|
||||
\ (Sanger/Illumina 1.9+ encoding) for quality trimming."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--phred64"
|
||||
description: "Instructs Cutadapt to use ASCII+64 quality scores as Phred scores\
|
||||
\ (Illumina 1.5 encoding) for quality trimming."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--fastqc"
|
||||
description: "Run FastQC in the default mode on the FastQ file once trimming is\
|
||||
\ complete."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--fastqc_args"
|
||||
description: "Passes extra arguments to FastQC. If more than one argument is to\
|
||||
\ be passed to FastQC they must be in the form \"arg1 arg2 ...\". Passing extra\
|
||||
\ arguments will automatically invoke FastQC, so --fastqc does not have to be\
|
||||
\ specified separately."
|
||||
info: null
|
||||
example:
|
||||
- "--nogroup --outdir /home/"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--adapter"
|
||||
alternatives:
|
||||
- "-a"
|
||||
description: "Adapter sequence to be trimmed. If not specified explicitly, Trim\
|
||||
\ Galore will try to auto-detect whether the Illumina universal, Nextera transposase\
|
||||
\ or Illumina small RNA adapter sequence was used. A single base may also be\
|
||||
\ given as e.g. -a A{10}, to be expanded to -a AAAAAAAAAA. \nAt a special request,\
|
||||
\ multiple adapters can also be specified like so: \n -a \" AGCTCCCG -a TTTCATTATAT\
|
||||
\ -a TTTATTCGGATTTAT\" -a2 \" AGCTAGCG -a TCTCTTATAT -a TTTCGGATTTAT\", \nor\
|
||||
\ so:\n -a \"file:../multiple_adapters.fa\" -a2 \"file:../different_adapters.fa\"\
|
||||
\nPotentially in conjucntion with the parameter \"-n 3\" to trim all adapters.\
|
||||
\ \n example: 20\n"
|
||||
info: null
|
||||
example:
|
||||
- "AGCTCCCG"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--adapter2"
|
||||
alternatives:
|
||||
- "-a2"
|
||||
description: "Optional adapter sequence to be trimmed off read 2 of paired-end\
|
||||
\ files. This option requires '--paired' to be specified as well. If the libraries\
|
||||
\ to be trimmed are smallRNA then a2 will be set to the Illumina small RNA 5'\
|
||||
\ adapter automatically (GATCGTCGGACT). A single base may also be given as e.g.\
|
||||
\ -a2 A{10}, to be expanded to -a2 AAAAAAAAAA."
|
||||
info: null
|
||||
example:
|
||||
- "AGCTCCCG"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--illumina"
|
||||
description: "Adapter sequence to be trimmed is the first 13bp of the Illumina\
|
||||
\ universal adapter 'AGATCGGAAGAGC' instead of the default auto-detection of\
|
||||
\ adapter sequence."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--stranded_illumina"
|
||||
description: "Adapter sequence to be trimmed is the first 13bp of the Illumina\
|
||||
\ stranded mRNA or Total RNA adapter 'ACTGTCTCTTATA' instead of the default\
|
||||
\ auto-detection of adapter sequence."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--nextera"
|
||||
description: "Adapter sequence to be trimmed is the first 12bp of the Nextera\
|
||||
\ adapter 'CTGTCTCTTATA' instead of the default auto-detection of adapter sequence."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--small_rna"
|
||||
description: "Adapter sequence to be trimmed is the first 12bp of the Illumina\
|
||||
\ Small RNA 3' Adapter 'TGGAATTCTCGG' instead of the default auto-detection\
|
||||
\ of adapter sequence. Selecting to trim smallRNA adapters will also lower the\
|
||||
\ --length value to 18bp. If the smallRNA libraries are paired-end then a automatically\
|
||||
\ (GATCGTCGGACT) unless -a 2 had been defined explicitly."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--consider_already_trimmed"
|
||||
description: "During adapter auto-detection, the limit set by this argument allows\
|
||||
\ the user to set a threshold up to which the file is considered already adapter-trimmed.\
|
||||
\ If no adapter sequence exceeds this threshold, no additional adapter trimming\
|
||||
\ will be performed (technically, the adapter is set to '-a X'). Quality trimming\
|
||||
\ is still performed as usual."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--max_length"
|
||||
description: "Discard reads that are longer than the specified value after trimming.\
|
||||
\ This is only advised for smallRNA sequencing to remove non-small RNA sequences."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--stringency"
|
||||
description: "Overlap with adapter sequence required to trim a sequence. Defaults\
|
||||
\ to a very stringent setting of 1, i.e. even a single bp of overlapping sequence\
|
||||
\ will be trimmed off from the 3' end of any read."
|
||||
info: null
|
||||
example:
|
||||
- 1
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "double"
|
||||
name: "--error_rate"
|
||||
alternatives:
|
||||
- "-e"
|
||||
description: "Maximum allowed error rate (no. of errors divided by the length\
|
||||
\ of the matching region)"
|
||||
info: null
|
||||
example:
|
||||
- 0.1
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--gzip"
|
||||
description: "Compress the output file with GZIP. If the input files are GZIP-compressed\
|
||||
\ the output files will automatically be GZIP compressed as well. As of v0.2.8\
|
||||
\ the compression will take place on the fly."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--dont_gzip"
|
||||
description: "Output files won't be compressed with GZIP. This option overrides\
|
||||
\ --gzip."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--length"
|
||||
description: "Discard reads that became shorter than the specified length because\
|
||||
\ of either quality or adapter trimming. A value of '0' effectively disables\
|
||||
\ this behaviour. For paired-end files, both reads of a read-pair need to be\
|
||||
\ longer than the specified length to be printed out to validated paired-end\
|
||||
\ files. If only one read became too short there is the possibility of keeping\
|
||||
\ such unpaired single-end reads using the --retain_unpaired option."
|
||||
info: null
|
||||
example:
|
||||
- 20
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--max_n"
|
||||
description: "The total number of Ns a read may contain before it will be removed\
|
||||
\ altogether.In a paired-end setting, either read exceeding this limit will\
|
||||
\ result in the entire pair being removed from the trimmed output files. If\
|
||||
\ COUNT is a number between 0 and 1, it is interpreted as a fraction of the\
|
||||
\ read length."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--trim_n"
|
||||
description: "Removes Ns from either side of the read. This option does currently\
|
||||
\ not work in RRBS mode."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--no_report_file"
|
||||
description: "If specified no report file will be generated."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--suppress_warn"
|
||||
description: "If specified any output to STDOUT or STDERR will be suppressed."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--clip_R1"
|
||||
description: "Instructs TrimGalore to remove given number of bp from the 5' end\
|
||||
\ of read 1 (or single-end reads). This may be useful if the qualities were\
|
||||
\ very poor, or if there is some sort of unwanted bias at the 5' end."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--clip_R2"
|
||||
description: "Instructs TrimGalore to remove given number bp from the 5' end of\
|
||||
\ read 2 (paired-end reads only). This may be useful if the qualities were very\
|
||||
\ poor, or if there is some sort of unwanted bias at the 5' end. For paired-end\
|
||||
\ BS-Seq, it is recommended to remove the first few bp because the end-repair\
|
||||
\ reaction may introduce a bias towards low methylation."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--three_prime_clip_R1"
|
||||
description: "Instructs Trim Galore to remove spacified number of bp from the\
|
||||
\ 3' end of read 1 (or single-end reads) AFTER adapter/quality trimming has\
|
||||
\ been performed. This may remove some bias from the 3' end that is not directly\
|
||||
\ related to adapter sequence or basecall quality."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--three_prime_clip_R2"
|
||||
description: "Instructs Trim Galore to remove <int> bp from the 3' end of read\
|
||||
\ 2 AFTER adapter/quality trimming has been performed. This may remove some\
|
||||
\ unwanted bias from the 3' end that is not directly related to adapter sequence\
|
||||
\ or basecall quality."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--nextseq"
|
||||
description: "This enables the option '--nextseq-trim=3'CUTOFF' within Cutadapt,\
|
||||
\ which will set a quality cutoff (that is normally given with -q instead),\
|
||||
\ but qualities of G bases are ignored. This trimming is in common for the NextSeq-\
|
||||
\ and NovaSeq-platforms, where basecalls without any signal are called as high-quality\
|
||||
\ G bases. This is mutually exlusive with '-q INT'."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--basename"
|
||||
description: "Use specified name (PREFERRED_NAME) as the basename for output files,\
|
||||
\ instead of deriving the filenames from the input files. Single-end data would\
|
||||
\ be called PREFERRED_NAME_trimmed.fq(.gz), or PREFERRED_NAME_val_1.fq(.gz)\
|
||||
\ and PREFERRED_NAME_val_2.fq(.gz) for paired-end data. --basename only works\
|
||||
\ when 1 file (single-end) or 2 files (paired-end) are specified, but not for\
|
||||
\ longer lists."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--cores"
|
||||
alternatives:
|
||||
- "-j"
|
||||
description: "Number of cores to be used for trimming"
|
||||
info: null
|
||||
example:
|
||||
- 1
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Specific trimming options without adapter/quality trimming"
|
||||
arguments:
|
||||
- type: "integer"
|
||||
name: "--hardtrim5"
|
||||
description: "Instead of performing adapter-/quality trimming, this option will\
|
||||
\ simply hard-trim sequences to <int> bp at the 5'-end. Once hard-trimming of\
|
||||
\ files is complete, Trim Galore will exit. Hard-trimmed output files will end\
|
||||
\ in .<int>_5prime.fq(.gz)."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--hardtrim3"
|
||||
description: "Instead of performing adapter-/quality trimming, this option will\
|
||||
\ simply hard-trim sequences to <int> bp at the 3'-end. Once hard-trimming of\
|
||||
\ files is complete, Trim Galore will exit. Hard-trimmed output files will end\
|
||||
\ in .<int>_3prime.fq(.gz)."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--clock"
|
||||
description: "In this mode, reads are trimmed in a specific way that is currently\
|
||||
\ used for the Mouse Epigenetic Clock."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--polyA"
|
||||
description: "This is a new, still experimental, trimming mode to identify and\
|
||||
\ remove poly-A tails from sequences. When --polyA is selected, Trim Galore\
|
||||
\ attempts to identify from the first supplied sample whether sequences contain\
|
||||
\ more often a stretch of either 'AAAAAAAAAA' or 'TTTTTTTTTT'. This determines\
|
||||
\ if Read 1 of a paired-end end file, or single-end files, are trimmed for PolyA\
|
||||
\ or PolyT. In case of paired-end sequencing, Read2 is trimmed for the complementary\
|
||||
\ base from the start of the reads. The auto-detection uses a default of A{20}\
|
||||
\ for Read1 (3'-end trimming) and T{150} for Read2 (5'-end trimming). These\
|
||||
\ values may be changed manually using the options -a and -a2. In addition to\
|
||||
\ trimming the sequences, white spaces are replaced with _ and it records in\
|
||||
\ the read ID how many bases were trimmed so it can later be used to identify\
|
||||
\ PolyA trimmed sequences. This is currently done by writing tags to both the\
|
||||
\ start (\"32:A:\") and end (\"_PolyA:32\") of the reads. The poly-A trimming\
|
||||
\ mode expects that sequences were both adapter and quality before looking\
|
||||
\ for Poly-A tails, and it is the user's responsibility to carry out an initial\
|
||||
\ round of trimming."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--implicon"
|
||||
description: "This is a special mode of operation for paired-end data, such as\
|
||||
\ required for the IMPLICON method, where a UMI sequence is getting transferred\
|
||||
\ from the start of Read 2 to the readID of both reads. Following this, Trim\
|
||||
\ Galore will exit. In it's current implementation, the UMI carrying reads come\
|
||||
\ in the following format\n Read 1 5' FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\
|
||||
\ 3'\n Read 2 3' UUUUUUUUFFFFFFFFFFFFFFFFFFFFFFFFFFFF 5'\nWhere UUUUUUUU is\
|
||||
\ a random 8-mer unique molecular identifier (UMI) and FFFFFFF... is the actual\
|
||||
\ fragment to be sequenced. The UMI of Read 2 (R2) is written into the read\
|
||||
\ ID of both reads and removed from the actual sequence.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "RRBS-specific options"
|
||||
arguments:
|
||||
- type: "boolean"
|
||||
name: "--rrbs"
|
||||
description: "Specifies that the input file was an MspI digested RRBS sample (recognition\
|
||||
\ site is CCGG). Single-end or Read 1 sequences (paired-end) which were adapter-trimmed\
|
||||
\ will have a further 2 bp removed from their 3' end. Sequences which were merely\
|
||||
\ trimmed because of poor quality will not be shortened further. Read 2 of paired-end\
|
||||
\ libraries will in addition have the first 2 bp removed from the 5' end (by\
|
||||
\ setting '--clip_r2 2'). This is to avoid using artificial methylation calls\
|
||||
\ from the filled-in cytosine positions close to the 3' MspI site in sequenced\
|
||||
\ fragments. This option is not recommended for users of the Tecan Ovation RRBS\
|
||||
\ Methyl-Seq with TrueMethyl oxBS 1-16 kit (see below)."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--non_directional"
|
||||
description: "Selecting this option for non-directional RRBS libraries will screen\
|
||||
\ quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and,\
|
||||
\ if found, removes the first two basepairs. Like with the option '--rrbs' this\
|
||||
\ avoids using cytosine positions that were filled-in during the end-repair\
|
||||
\ step. '--non_directional' requires '--rrbs' to be specified as well. Note\
|
||||
\ that this option does not set '--clip_r2 2' in paired-end mode."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--keep"
|
||||
description: "Keep the quality trimmed intermediate file."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Paired-end specific options"
|
||||
arguments:
|
||||
- type: "boolean"
|
||||
name: "--paired"
|
||||
description: "This option performs length trimming of quality/adapter/RRBS trimmed\
|
||||
\ reads for paired-end files. To pass the validation test, both sequences of\
|
||||
\ a sequence pair are required to have a certain minimum length which is governed\
|
||||
\ by the option --length (see above). If only one read passes this length threshold\
|
||||
\ the other read can be rescued (see option --retain_unpaired). Using this option\
|
||||
\ lets you discard too short read pairs without disturbing the sequence-by-sequence\
|
||||
\ order of FastQ files which is required by many aligners. Trim Galore expects\
|
||||
\ paired-end files to be supplied in a pairwise fashion, e.g. file1_1.fq file1_2.fq\
|
||||
\ SRR2_1.fq.gz SRR2_2.fq.gz ... ."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--retain_unpaired"
|
||||
description: "If only one of the two paired-end reads became too short, the longer\
|
||||
\ read will be written to either '.unpaired_1.fq' or '.unpaired_2.fq' output\
|
||||
\ files. The length cutoff for unpaired single-end reads is governed by the\
|
||||
\ parameters -r1/--length_1 and -r2/--length_2."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--length_1"
|
||||
alternatives:
|
||||
- "-r1"
|
||||
description: "Unpaired single-end read length cutoff needed for read 1 to be written\
|
||||
\ to '.unpaired_1.fq' output file. These reads may be mapped in single-end mode."
|
||||
info: null
|
||||
example:
|
||||
- 35
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--length_2"
|
||||
alternatives:
|
||||
- "-r2"
|
||||
description: "Unpaired single-end read length cutoff needed for read 2 to be written\
|
||||
\ to '.unpaired_2.fq' output file. These reads may be mapped in single-end mode."
|
||||
info: null
|
||||
example:
|
||||
- 35
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output_dir"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "If specified all output will be written to this directory instead\
|
||||
\ of the current directory."
|
||||
info: null
|
||||
default:
|
||||
- "trimmed_output"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--trimmed_r1"
|
||||
description: "Output file for read 1. Only works when 1 file (single-end) or 2\
|
||||
\ files (paired-end) are specified, but not for longer lists."
|
||||
info: null
|
||||
example:
|
||||
- "read_1.fastq.gz"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--trimmed_r2"
|
||||
description: "Output file for read 2. Only works when 1 file (single-end) or 2\
|
||||
\ files (paired-end) are specified, but not for longer lists."
|
||||
info: null
|
||||
example:
|
||||
- "read_2.fastq.gz"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--trimming_report_r1"
|
||||
description: "Trimming report for read 1. Only works when 1 file (single-end)\
|
||||
\ or 2 files (paired-end) are specified, but not for longer lists."
|
||||
info: null
|
||||
example:
|
||||
- "read_1.trimming_report.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--trimming_report_r2"
|
||||
description: "Trimming report for read 1. Only works when 1 file (single-end)\
|
||||
\ or 2 files (paired-end) are specified, but not for longer lists."
|
||||
info: null
|
||||
example:
|
||||
- "read_2.trimming_report.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--trimmed_fastqc_html_1"
|
||||
description: "FastQC report for trimmed (single-end) reads (or read 1 for paired-end).\
|
||||
\ Only works when 1 file (single-end) or 2 files (paired-end) are specified,\
|
||||
\ but not for longer lists."
|
||||
info: null
|
||||
example:
|
||||
- "read_1.fastqc.html"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--trimmed_fastqc_html_2"
|
||||
description: "FastQC report for trimmed reads (read2 for paired-end). Only works\
|
||||
\ when 1 file (single-end) or 2 files (paired-end) are specified, but not for\
|
||||
\ longer lists."
|
||||
info: null
|
||||
example:
|
||||
- "read_2.fastqc.html"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--trimmed_fastqc_zip_1"
|
||||
description: "FastQC results for trimmed (single-end) reads (or read 1 for paired-end).\
|
||||
\ Only works when 1 file (single-end) or 2 files (paired-end) are specified,\
|
||||
\ but not for longer lists."
|
||||
info: null
|
||||
example:
|
||||
- "read_1.fastqc.zip"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--trimmed_fastqc_zip_2"
|
||||
description: "FastQC results for trimmed reads (read2 for paired-end). Only works\
|
||||
\ when 1 file (single-end) or 2 files (paired-end) are specified, but not for\
|
||||
\ longer lists."
|
||||
info: null
|
||||
example:
|
||||
- "read_2.fastqc.zip"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--unpaired_r1"
|
||||
description: "Output file for unpired read 1. Only works when 1 file (single-end)\
|
||||
\ or 2 files (paired-end) are specified, but not for longer lists."
|
||||
info: null
|
||||
example:
|
||||
- "unpaired_read_1.fastq"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--unpaired_r2"
|
||||
description: "Output file for unpaired read 2. Only works when 1 file (single-end)\
|
||||
\ or 2 files (paired-end) are specified, but not for longer lists."
|
||||
info: null
|
||||
example:
|
||||
- "unpaired_read_2.fastq"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "A wrapper tool around Cutadapt and FastQC to consistently apply quality\
|
||||
\ and adapter trimming to FastQ files. \n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
keywords:
|
||||
- "trimming"
|
||||
- "adapters"
|
||||
license: "GPL-3.0"
|
||||
links:
|
||||
repository: "https://github.com/FelixKrueger/TrimGalore"
|
||||
homepage: "https://github.com/FelixKrueger/TrimGalore"
|
||||
documentation: "https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "quay.io/biocontainers/trim-galore:0.6.9--hdfd78af_0"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "docker"
|
||||
run:
|
||||
- "echo \"TrimGalore: `trim_galore --version | sed -n 's/.*version\\s\\+\\([0-9]\\\
|
||||
+\\.[0-9]\\+\\.[0-9]\\+\\).*/\\1/p'`\" > /var/software_versions.txt\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/trimgalore/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/trimgalore"
|
||||
executable: "target/executable/trimgalore/trimgalore"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -87,7 +87,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -185,8 +185,8 @@ build_info:
|
||||
output: "target/executable/tx2gene"
|
||||
executable: "target/executable/tx2gene/tx2gene"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -197,7 +197,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -483,9 +483,9 @@ RUN apt-get update && \
|
||||
RUN pip install --upgrade pip
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component tx2gene"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:31Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:50Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -146,7 +146,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -251,8 +251,8 @@ build_info:
|
||||
output: "target/executable/tximport"
|
||||
executable: "target/executable/tximport/tximport"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -263,7 +263,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -508,9 +508,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
|
||||
Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")'
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component tximport"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:30Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:51Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -137,5 +137,6 @@ if ("tx2gene" %in% names(transcript_info) && !is.null(transcript_info$tx2gene))
|
||||
done <- lapply(params, write_se_table)
|
||||
|
||||
# Output session information and citations
|
||||
citation("tximeta")
|
||||
# Removed for now because the 'tximeta' package is not found sometimes
|
||||
# citation("tximeta")
|
||||
sessionInfo()
|
||||
@@ -65,7 +65,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -164,8 +164,8 @@ build_info:
|
||||
output: "target/executable/ucsc/bedclip"
|
||||
executable: "target/executable/ucsc/bedclip/bedclip"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -176,7 +176,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -473,9 +473,9 @@ RUN apt-get update && \
|
||||
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:30Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:50Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -65,7 +65,7 @@ requirements:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -164,8 +164,8 @@ build_info:
|
||||
output: "target/executable/ucsc/bedgraphtobigwig"
|
||||
executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -176,7 +176,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -473,9 +473,9 @@ RUN apt-get update && \
|
||||
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T08:42:31Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
LABEL org.opencontainers.image.created="2024-11-27T11:43:50Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -1,225 +0,0 @@
|
||||
name: "umitools_dedup"
|
||||
namespace: "umitools"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "boolean"
|
||||
name: "--paired"
|
||||
description: "Paired fastq files or not?"
|
||||
info: null
|
||||
default:
|
||||
- false
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--bam"
|
||||
description: "Input BAM file"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--bai"
|
||||
description: "BAM index"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--get_output_stats"
|
||||
description: "Whether or not to generate output stats."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output_bam"
|
||||
description: "Deduplicated BAM file"
|
||||
info: null
|
||||
default:
|
||||
- "$id.$key.bam"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_stats"
|
||||
description: "Directory containing UMI based dedupllication statistics files"
|
||||
info: null
|
||||
default:
|
||||
- "$id.umi_dedup.stats"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "Deduplicate reads based on the mapping co-ordinate and the UMI attached\
|
||||
\ to the read.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "chr19.bam"
|
||||
- type: "file"
|
||||
path: "chr19.bam.bai"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/umitools/dedup/main.nf"
|
||||
- "modules/nf-core/umitools/dedup/meta.yml"
|
||||
last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "pip"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "umi_tools"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/umitools/umitools_dedup/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/umitools/umitools_dedup"
|
||||
executable: "target/executable/umitools/umitools_dedup/umitools_dedup"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,283 +0,0 @@
|
||||
name: "umitools_extract"
|
||||
namespace: "umitools"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "boolean"
|
||||
name: "--paired"
|
||||
description: "Paired fastq files or not?"
|
||||
info: null
|
||||
default:
|
||||
- false
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "Input fastq files, either one or two (paired)"
|
||||
info: null
|
||||
example:
|
||||
- "sample.fastq"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ","
|
||||
- type: "string"
|
||||
name: "--bc_pattern"
|
||||
description: "The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the\
|
||||
\ first 6 nucleotides of the read are from the UMI."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ","
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--fastq_1"
|
||||
description: "Output file for read 1."
|
||||
info: null
|
||||
default:
|
||||
- "$id.$key.read_1.fastq"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--fastq_2"
|
||||
description: "Output file for read 2."
|
||||
info: null
|
||||
default:
|
||||
- "$id.$key.read_2.fastq"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Optional arguments"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--umitools_extract_method"
|
||||
description: "UMI pattern to use."
|
||||
info: null
|
||||
default:
|
||||
- "string"
|
||||
required: false
|
||||
choices:
|
||||
- "string"
|
||||
- "regex"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--umitools_umi_separator"
|
||||
description: "The character that separates the UMI in the read name. Most likely\
|
||||
\ a colon if you skipped the extraction with UMI-tools and used other software."
|
||||
info: null
|
||||
default:
|
||||
- "_"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--umitools_grouping_method"
|
||||
description: "Method to use to determine read groups by subsuming those with similar\
|
||||
\ UMIs. All methods start by identifying the reads with the same mapping position,\
|
||||
\ but treat similar yet nonidentical UMIs differently."
|
||||
info: null
|
||||
default:
|
||||
- "directional"
|
||||
required: false
|
||||
choices:
|
||||
- "unique"
|
||||
- "percentile"
|
||||
- "cluster"
|
||||
- "adjacency"
|
||||
- "directional"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--umi_discard_read"
|
||||
description: "After UMI barcode extraction discard either R1 or R2 by setting\
|
||||
\ this parameter to 1 or 2, respectively."
|
||||
info: null
|
||||
default:
|
||||
- 0
|
||||
required: false
|
||||
choices:
|
||||
- 0
|
||||
- 1
|
||||
- 2
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "UMI-tools contains tools for dealing with Unique Molecular Identifiers\
|
||||
\ (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes. See\
|
||||
\ https://umi-tools.readthedocs.io/en/latest/ for more information.\nThis component\
|
||||
\ flexible removes UMI sequences from fastq reads. UMIs are removed and appended\
|
||||
\ to the read name.\nThis component extracts UMI barcode from a read and add it\
|
||||
\ to the read name, leaving any sample barcode in place\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "scrb_seq_fastq.1.gz"
|
||||
- type: "file"
|
||||
path: "scrb_seq_fastq.2.gz"
|
||||
- type: "file"
|
||||
path: "slim.fastq.gz"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/nf-core/umitools/extract/main.nf"
|
||||
- "modules/nf-core/umitools/extract/meta.yml"
|
||||
last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "pip"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "umi_tools"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/umitools/umitools_extract/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/umitools/umitools_extract"
|
||||
executable: "target/executable/umitools/umitools_extract/umitools_extract"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,186 +0,0 @@
|
||||
name: "umitools_prepareforquant"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--bam"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
info: null
|
||||
default:
|
||||
- "$id.transcriptome_sorted.bam"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--log"
|
||||
info: null
|
||||
default:
|
||||
- "$id.$key.log"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "prepare-for-rsem.py"
|
||||
description: "Fix paired-end reads in name sorted BAM file to prepare for salmon quantification"
|
||||
info:
|
||||
migration_info:
|
||||
git_repo: "https://github.com/nf-core/rnaseq.git"
|
||||
paths:
|
||||
- "modules/local/umitools_prepareforrsem.nf"
|
||||
last_sha: "0a1bdcfbb498987643b74e9fccab85ccd9f2a17d"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "pip"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "umi_tools"
|
||||
- "pysam"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/umitools_prepareforquant/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/umitools_prepareforquant"
|
||||
executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
organization: "vsh"
|
||||
@@ -1,270 +0,0 @@
|
||||
#!/usr/bin/env python3
|
||||
|
||||
"""
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
Credits
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
This script is a clone of the "prepare-for-rsem.py" script written by
|
||||
Ian Sudbury, Tom Smith and other contributors to the UMI-tools package:
|
||||
https://github.com/CGATOxford/UMI-tools
|
||||
|
||||
It has been included here to address problems encountered with
|
||||
Salmon quant and RSEM as discussed in the issue below:
|
||||
https://github.com/CGATOxford/UMI-tools/issues/465
|
||||
|
||||
When the "umi_tools prepare-for-rsem" command becomes available in an official
|
||||
UMI-tools release this script will be replaced and deprecated.
|
||||
|
||||
Commit:
|
||||
https://github.com/CGATOxford/UMI-tools/blob/bf8608d6a172c5ca0dcf33c126b4e23429177a72/umi_tools/prepare-for-rsem.py
|
||||
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
prepare_for_rsem - make the output from dedup or group compatible with RSEM
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
The SAM format specification states that the mnext and mpos fields should point
|
||||
to the primary alignment of a read's mate. However, not all aligners adhere to
|
||||
this standard. In addition, the RSEM software requires that the mate of a read1
|
||||
appears directly after it in its input BAM. This requires that there is exactly
|
||||
one read1 alignment for every read2 and vice versa.
|
||||
|
||||
In general (except in a few edge cases) UMI tools outputs only the read2 to that
|
||||
corresponds to the read specified in the mnext and mpos positions of a selected
|
||||
read1, and only outputs this read once, even if multiple read1s point to it.
|
||||
This makes UMI-tools outputs incompatible with RSEM. This script takes the output
|
||||
from dedup or groups and ensures that each read1 has exactly one read2 (and vice
|
||||
versa), that read2 always appears directly after read1,and that pairs point to
|
||||
each other (note this is technically not valid SAM format). Copy any specified
|
||||
tags from read1 to read2 if they are present (by default, UG and BX, the unique
|
||||
group and correct UMI tags added by _group_)
|
||||
|
||||
Input must to name sorted.
|
||||
|
||||
|
||||
https://raw.githubusercontent.com/CGATOxford/UMI-tools/master/LICENSE
|
||||
|
||||
"""
|
||||
|
||||
from umi_tools import Utilities as U
|
||||
from collections import defaultdict, Counter
|
||||
import pysam
|
||||
import sys
|
||||
|
||||
usage = """
|
||||
prepare_for_rsem - make output from dedup or group compatible with RSEM
|
||||
|
||||
Usage: umi_tools prepare_for_rsem [OPTIONS] [--stdin=IN_BAM] [--stdout=OUT_BAM]
|
||||
|
||||
note: If --stdout is omited, standard out is output. To
|
||||
generate a valid BAM file on standard out, please
|
||||
redirect log with --log=LOGFILE or --log2stderr """
|
||||
|
||||
|
||||
def chunk_bam(bamfile):
|
||||
"""Take in a iterator of pysam.AlignmentSegment entries and yield
|
||||
lists of reads that all share the same name"""
|
||||
|
||||
last_query_name = None
|
||||
output_buffer = list()
|
||||
|
||||
for read in bamfile:
|
||||
if last_query_name is not None and last_query_name != read.query_name:
|
||||
yield (output_buffer)
|
||||
output_buffer = list()
|
||||
|
||||
last_query_name = read.query_name
|
||||
output_buffer.append(read)
|
||||
|
||||
yield (output_buffer)
|
||||
|
||||
|
||||
def copy_tags(tags, read1, read2):
|
||||
"""Given a list of tags, copies the values of these tags from read1
|
||||
to read2, if the tag is set"""
|
||||
|
||||
for tag in tags:
|
||||
try:
|
||||
read1_tag = read1.get_tag(tag, with_value_type=True)
|
||||
read2.set_tag(tag, value=read1_tag[0], value_type=read1_tag[1])
|
||||
except KeyError:
|
||||
pass
|
||||
|
||||
return read2
|
||||
|
||||
|
||||
def pick_mate(read, template_dict, mate_key):
|
||||
"""Find the mate of read in the template dict using key. It will retrieve
|
||||
all reads at that key, and then scan to pick the one that refers to _read_
|
||||
as it's mate. If there is no such read, it picks a first one it comes to"""
|
||||
|
||||
mate = None
|
||||
|
||||
# get a list of secondary reads at the correct alignment position
|
||||
potential_mates = template_dict[not read.is_read1][mate_key]
|
||||
|
||||
# search through one at a time to find a read that points to the current read
|
||||
# as its mate.
|
||||
for candidate_mate in potential_mates:
|
||||
if (
|
||||
candidate_mate.next_reference_name == read.reference_name
|
||||
and candidate_mate.next_reference_start == read.pos
|
||||
):
|
||||
mate = candidate_mate
|
||||
|
||||
# if no such read is found, then pick any old secondary alignment at that position
|
||||
# note: this happens when UMI-tools outputs the wrong read as something's pair.
|
||||
if mate is None and len(potential_mates) > 0:
|
||||
mate = potential_mates[0]
|
||||
|
||||
return mate
|
||||
|
||||
|
||||
def main(argv=None):
|
||||
if argv is None:
|
||||
argv = sys.argv
|
||||
|
||||
# setup command line parser
|
||||
parser = U.OptionParser(version="%prog version: $Id$", usage=usage, description=globals()["__doc__"])
|
||||
group = U.OptionGroup(parser, "RSEM preparation specific options")
|
||||
|
||||
group.add_option(
|
||||
"--tags",
|
||||
dest="tags",
|
||||
type="string",
|
||||
default="UG,BX",
|
||||
help="Comma-separated list of tags to transfer from read1 to read2",
|
||||
)
|
||||
group.add_option(
|
||||
"--sam", dest="sam", action="store_true", default=False, help="input and output SAM rather than BAM"
|
||||
)
|
||||
|
||||
parser.add_option_group(group)
|
||||
|
||||
# add common options (-h/--help, ...) and parse command line
|
||||
(options, args) = U.Start(
|
||||
parser, argv=argv, add_group_dedup_options=False, add_umi_grouping_options=False, add_sam_options=False
|
||||
)
|
||||
|
||||
skipped_stats = Counter()
|
||||
|
||||
if options.stdin != sys.stdin:
|
||||
in_name = options.stdin.name
|
||||
options.stdin.close()
|
||||
else:
|
||||
in_name = "-"
|
||||
|
||||
if options.sam:
|
||||
mode = ""
|
||||
else:
|
||||
mode = "b"
|
||||
|
||||
inbam = pysam.AlignmentFile(in_name, "r" + mode)
|
||||
|
||||
if options.stdout != sys.stdout:
|
||||
out_name = options.stdout.name
|
||||
options.stdout.close()
|
||||
else:
|
||||
out_name = "-"
|
||||
|
||||
outbam = pysam.AlignmentFile(out_name, "w" + mode, template=inbam)
|
||||
|
||||
options.tags = options.tags.split(",")
|
||||
|
||||
for template in chunk_bam(inbam):
|
||||
assert len(set(r.query_name for r in template)) == 1
|
||||
current_template = {True: defaultdict(list), False: defaultdict(list)}
|
||||
|
||||
for read in template:
|
||||
key = (read.reference_name, read.pos, not read.is_secondary)
|
||||
current_template[read.is_read1][key].append(read)
|
||||
|
||||
output = set()
|
||||
|
||||
for read in template:
|
||||
mate = None
|
||||
|
||||
# if this read is a non_primary alignment, we first want to check if it has a mate
|
||||
# with the non-primary alignment flag set.
|
||||
|
||||
mate_key_primary = True
|
||||
mate_key_secondary = (read.next_reference_name, read.next_reference_start, False)
|
||||
|
||||
# First look for a read that has the same primary/secondary status
|
||||
# as read (i.e. secondary mate for secondary read, and primary mate
|
||||
# for primary read)
|
||||
mate_key = (read.next_reference_name, read.next_reference_start, read.is_secondary)
|
||||
mate = pick_mate(read, current_template, mate_key)
|
||||
|
||||
# If none was found then look for the opposite (primary mate of secondary
|
||||
# read or seconadary mate of primary read)
|
||||
if mate is None:
|
||||
mate_key = (read.next_reference_name, read.next_reference_start, not read.is_secondary)
|
||||
mate = pick_mate(read, current_template, mate_key)
|
||||
|
||||
# If we still don't have a mate, then their can't be one?
|
||||
if mate is None:
|
||||
skipped_stats["no_mate"] += 1
|
||||
U.warn(
|
||||
"Alignment {} has no mate -- skipped".format(
|
||||
"\t".join(map(str, [read.query_name, read.flag, read.reference_name, int(read.pos)]))
|
||||
)
|
||||
)
|
||||
continue
|
||||
|
||||
# because we might want to make changes to the read, but not have those changes reflected
|
||||
# if we need the read again,we copy the read. This is only way I can find to do this.
|
||||
read = pysam.AlignedSegment().from_dict(read.to_dict(), read.header)
|
||||
mate = pysam.AlignedSegment().from_dict(mate.to_dict(), read.header)
|
||||
|
||||
# Make it so that if our read is secondary, the mate is also secondary. We don't make the
|
||||
# mate primary if the read is primary because we would otherwise end up with mulitple
|
||||
# primary alignments.
|
||||
if read.is_secondary:
|
||||
mate.is_secondary = True
|
||||
|
||||
# In a situation where there is already one mate for each read, then we will come across
|
||||
# each pair twice - once when we scan read1 and once when we scan read2. Thus we need
|
||||
# to make sure we don't output something already output.
|
||||
if read.is_read1:
|
||||
mate = copy_tags(options.tags, read, mate)
|
||||
output_key = str(read) + str(mate)
|
||||
|
||||
if output_key not in output:
|
||||
output.add(output_key)
|
||||
outbam.write(read)
|
||||
outbam.write(mate)
|
||||
skipped_stats["pairs_output"] += 1
|
||||
|
||||
elif read.is_read2:
|
||||
read = copy_tags(options.tags, mate, read)
|
||||
output_key = str(mate) + str(read)
|
||||
|
||||
if output_key not in output:
|
||||
output.add(output_key)
|
||||
outbam.write(mate)
|
||||
outbam.write(read)
|
||||
skipped_stats["pairs_output"] += 1
|
||||
|
||||
else:
|
||||
skipped_stats["skipped_not_read_12"] += 1
|
||||
U.warn(
|
||||
"Alignment {} is neither read1 nor read2 -- skipped".format(
|
||||
"\t".join(map(str, [read.query_name, read.flag, read.reference_name, int(read.pos)]))
|
||||
)
|
||||
)
|
||||
continue
|
||||
|
||||
if not out_name == "-":
|
||||
outbam.close()
|
||||
|
||||
U.info(
|
||||
"Total pairs output: {}, Pairs skipped - no mates: {},"
|
||||
" Pairs skipped - not read1 or 2: {}".format(
|
||||
skipped_stats["pairs_output"], skipped_stats["no_mate"], skipped_stats["skipped_not_read12"]
|
||||
)
|
||||
)
|
||||
U.Stop()
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
sys.exit(main(sys.argv))
|
||||
File diff suppressed because it is too large
Load Diff
@@ -459,51 +459,57 @@ dependencies:
|
||||
- name: "star/star_align_reads"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_sort"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_index"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_stats"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_flagstat"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_idxstats"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "umitools/umitools_dedup"
|
||||
- name: "umi_tools/umi_tools_dedup"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "umitools_prepareforquant"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "umi_tools/umi_tools_prepareforrsem"
|
||||
repository:
|
||||
type: "local"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "salmon/salmon_quant"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "rsem/rsem_calculate_expression"
|
||||
repository:
|
||||
type: "local"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -584,8 +590,8 @@ build_info:
|
||||
output: "target/executable/workflows/genome_alignment_and_quant"
|
||||
executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"
|
||||
@@ -593,10 +599,10 @@ build_info:
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats"
|
||||
- "target/nextflow/umitools/umitools_dedup"
|
||||
- "target/nextflow/umitools_prepareforquant"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_dedup"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_prepareforrsem"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
|
||||
- "target/nextflow/rsem/rsem_calculate_expression"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_calculate_expression"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -607,7 +613,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -1285,16 +1285,16 @@ fi
|
||||
|
||||
|
||||
# set dependency paths
|
||||
VIASH_DEP_UMITOOLS_UMITOOLS_DEDUP="$VIASH_META_RESOURCES_DIR/../../../nextflow/umitools/umitools_dedup/main.nf"
|
||||
VIASH_DEP_UMITOOLS_PREPAREFORQUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/umitools_prepareforquant/main.nf"
|
||||
VIASH_DEP_RSEM_RSEM_CALCULATE_EXPRESSION="$VIASH_META_RESOURCES_DIR/../../../nextflow/rsem/rsem_calculate_expression/main.nf"
|
||||
VIASH_DEP_STAR_STAR_ALIGN_READS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf"
|
||||
VIASH_DEP_UMI_TOOLS_UMI_TOOLS_DEDUP="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_dedup/main.nf"
|
||||
VIASH_DEP_UMI_TOOLS_UMI_TOOLS_PREPAREFORRSEM="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf"
|
||||
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf"
|
||||
VIASH_DEP_RSEM_RSEM_CALCULATE_EXPRESSION="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_calculate_expression/main.nf"
|
||||
|
||||
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
||||
cat << VIASHEOF | eval $VIASH_CMD
|
||||
@@ -1400,167 +1400,169 @@ workflow run_wf {
|
||||
key: "genome_idxstats"
|
||||
)
|
||||
|
||||
//
|
||||
// Remove duplicate reads from BAM file based on UMIs
|
||||
//
|
||||
|
||||
// Deduplicate genome BAM file
|
||||
| umitools_dedup.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"paired": "paired",
|
||||
"bam": "genome_bam_sorted",
|
||||
"bai": "genome_bam_index",
|
||||
"get_output_stats": "umi_dedup_stats"
|
||||
],
|
||||
toState: [ "genome_bam_sorted": "output_bam" ],
|
||||
key: "genome_deduped"
|
||||
)
|
||||
| samtools_index.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"input": "genome_bam_sorted",
|
||||
"csi": "bam_csi_index"
|
||||
],
|
||||
toState: [ "genome_bam_index": "output" ],
|
||||
key: "genome_deduped"
|
||||
)
|
||||
| samtools_stats.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"input": "genome_bam_sorted",
|
||||
"bai": "genome_bam_index",
|
||||
"fasta": "fasta"
|
||||
],
|
||||
toState: [ "genome_bam_stats": "output" ],
|
||||
key: "genome_deduped_stats"
|
||||
)
|
||||
| samtools_flagstat.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"bam": "genome_bam_sorted",
|
||||
"bai": "genome_bam_index",
|
||||
"fasta": "fasta"
|
||||
],
|
||||
toState: [ "genome_bam_flagstat": "output" ],
|
||||
key: "genome_deduped_flagstat"
|
||||
)
|
||||
| samtools_idxstats.run(
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"bam": "genome_bam_sorted",
|
||||
"bai": "genome_bam_index",
|
||||
"fasta": "fasta",
|
||||
],
|
||||
toState: [ "genome_bam_idxstats": "output" ],
|
||||
key: "genome_deduped_idxstats"
|
||||
)
|
||||
//
|
||||
// Remove duplicate reads from BAM file based on UMIs
|
||||
//
|
||||
|
||||
// Deduplicate genome BAM file
|
||||
| umi_tools_dedup.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: { id, state ->
|
||||
def output_stats = state.umi_dedup_stats ? state.id :
|
||||
[ paired: state.paired,
|
||||
input: state.genome_bam,
|
||||
bai: state.genome_bam_index,
|
||||
output_stats: output_stats]
|
||||
},
|
||||
toState: [ "genome_bam_sorted": "output" ],
|
||||
key: "genome_deduped"
|
||||
)
|
||||
| samtools_index.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"input": "genome_bam_sorted",
|
||||
"csi": "bam_csi_index"
|
||||
],
|
||||
toState: [ "genome_bam_index": "output" ],
|
||||
key: "genome_deduped"
|
||||
)
|
||||
| samtools_stats.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"input": "genome_bam_sorted",
|
||||
"bai": "genome_bam_index",
|
||||
"fasta": "fasta"
|
||||
],
|
||||
toState: [ "genome_bam_stats": "output" ],
|
||||
key: "genome_deduped_stats"
|
||||
)
|
||||
| samtools_flagstat.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"bam": "genome_bam_sorted",
|
||||
"bai": "genome_bam_index",
|
||||
"fasta": "fasta"
|
||||
],
|
||||
toState: [ "genome_bam_flagstat": "output" ],
|
||||
key: "genome_deduped_flagstat"
|
||||
)
|
||||
| samtools_idxstats.run(
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"bam": "genome_bam_sorted",
|
||||
"bai": "genome_bam_index",
|
||||
"fasta": "fasta",
|
||||
],
|
||||
toState: [ "genome_bam_idxstats": "output" ],
|
||||
key: "genome_deduped_idxstats"
|
||||
)
|
||||
|
||||
// Deduplicate transcriptome BAM file
|
||||
|
||||
| samtools_sort.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [ "input": "transcriptome_bam" ],
|
||||
toState: [ "transcriptome_bam": "output" ],
|
||||
key: "transcriptome_sorted"
|
||||
)
|
||||
| samtools_index.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"input": "transcriptome_bam",
|
||||
"csi": "bam_csi_index"
|
||||
],
|
||||
toState: [ "transcriptome_bam_index": "output" ],
|
||||
key: "transcriptome_sorted"
|
||||
)
|
||||
| samtools_stats.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"input": "transcriptome_bam",
|
||||
"bai": "transcriptome_bam_index",
|
||||
],
|
||||
toState: [ "transcriptome_bam_stats": "output" ],
|
||||
key: "transcriptome_stats"
|
||||
)
|
||||
| samtools_flagstat.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"bam": "transcriptome_bam",
|
||||
"bai": "transcriptome_bam_index"
|
||||
],
|
||||
toState: [ "transcriptome_bam_flagstat": "output" ],
|
||||
key: "transcriptome_flagstat"
|
||||
)
|
||||
| samtools_idxstats.run(
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"bam": "transcriptome_bam",
|
||||
"bai": "transcriptome_bam_index"
|
||||
],
|
||||
toState: [ "transcriptome_bam_idxstats": "output" ],
|
||||
key: "transcriptome_idxstats"
|
||||
)
|
||||
|
||||
| umitools_dedup.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"paired": "paired",
|
||||
"bam": "transcriptome_bam",
|
||||
"bai": "transcriptome_bam_index",
|
||||
"get_output_stats": "umi_dedup_stats",
|
||||
],
|
||||
toState: [ "transcriptome_bam_deduped": "output_bam" ],
|
||||
key: "transcriptome_deduped"
|
||||
)
|
||||
| samtools_sort.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [ "input": "transcriptome_bam_deduped" ],
|
||||
toState: [ "transcriptome_bam": "output" ],
|
||||
key: "transcriptome_deduped_sorted"
|
||||
)
|
||||
| samtools_index.run (
|
||||
| samtools_sort.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [ "input": "transcriptome_bam" ],
|
||||
toState: [ "transcriptome_bam": "output" ],
|
||||
key: "transcriptome_sorted"
|
||||
)
|
||||
| samtools_index.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"input": "transcriptome_bam",
|
||||
"csi": "bam_csi_index"
|
||||
],
|
||||
toState: [ "transcriptome_bam_index": "output" ],
|
||||
key: "transcriptome_sorted"
|
||||
)
|
||||
| samtools_stats.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"input": "transcriptome_bam",
|
||||
"bai": "transcriptome_bam_index",
|
||||
],
|
||||
toState: [ "transcriptome_bam_stats": "output" ],
|
||||
key: "transcriptome_stats"
|
||||
)
|
||||
| samtools_flagstat.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"bam": "transcriptome_bam",
|
||||
"bai": "transcriptome_bam_index"
|
||||
],
|
||||
toState: [ "transcriptome_bam_flagstat": "output" ],
|
||||
key: "transcriptome_flagstat"
|
||||
)
|
||||
| samtools_idxstats.run(
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"bam": "transcriptome_bam",
|
||||
"bai": "transcriptome_bam_index"
|
||||
],
|
||||
toState: [ "transcriptome_bam_idxstats": "output" ],
|
||||
key: "transcriptome_idxstats"
|
||||
)
|
||||
|
||||
| umi_tools_dedup.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: { id, state ->
|
||||
def output_stats = state.umi_dedup_stats ? state.id :
|
||||
[ paired: state.paired,
|
||||
input: state.transcriptome_bam,
|
||||
bai: state.transcriptome_bam_index,
|
||||
output_stats: output_stats]
|
||||
},
|
||||
toState: [ "transcriptome_bam_deduped": "output" ],
|
||||
key: "transcriptome_deduped"
|
||||
)
|
||||
| samtools_sort.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [ "input": "transcriptome_bam_deduped" ],
|
||||
toState: [ "transcriptome_bam": "output" ],
|
||||
key: "transcriptome_deduped_sorted"
|
||||
)
|
||||
| samtools_stats.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"input": "transcriptome_bam",
|
||||
"bai": "transcriptome_bam_index"
|
||||
],
|
||||
toState: [ "transcriptome_bam_stats": "output" ],
|
||||
key: "transcriptome_deduped_stats"
|
||||
)
|
||||
| samtools_flagstat.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"bam": "transcriptome_bam",
|
||||
"bai": "transcriptome_bam_index"
|
||||
],
|
||||
toState: [ "transcriptome_bam_flagstat": "output" ],
|
||||
key: "transcriptome_deduped_flagstat"
|
||||
)
|
||||
| samtools_idxstats.run(
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"bam": "transcriptome_bam",
|
||||
"bai": "transcriptome_bam_index"
|
||||
],
|
||||
toState: [ "transcriptome_bam_idxstats": "output" ],
|
||||
key: "transcriptome_deduped_idxstats"
|
||||
)
|
||||
)
|
||||
| samtools_index.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"input": "transcriptome_bam",
|
||||
"csi": "bam_csi_index"
|
||||
],
|
||||
toState: [ "transcriptome_bam_index": "output" ],
|
||||
key: "transcriptome_deduped_sorted"
|
||||
)
|
||||
| samtools_stats.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"input": "transcriptome_bam",
|
||||
"bai": "transcriptome_bam_index"
|
||||
],
|
||||
toState: [ "transcriptome_bam_stats": "output" ],
|
||||
key: "transcriptome_deduped_stats"
|
||||
)
|
||||
| samtools_flagstat.run (
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"bam": "transcriptome_bam",
|
||||
"bai": "transcriptome_bam_index"
|
||||
],
|
||||
toState: [ "transcriptome_bam_flagstat": "output" ],
|
||||
key: "transcriptome_deduped_flagstat"
|
||||
)
|
||||
| samtools_idxstats.run(
|
||||
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
|
||||
fromState: [
|
||||
"bam": "transcriptome_bam",
|
||||
"bai": "transcriptome_bam_index"
|
||||
],
|
||||
toState: [ "transcriptome_bam_idxstats": "output" ],
|
||||
key: "transcriptome_deduped_idxstats"
|
||||
)
|
||||
|
||||
// Fix paired-end reads in name sorted BAM file
|
||||
| umitools_prepareforquant.run (
|
||||
runIf: { id, state -> state.with_umi && state.paired && state.aligner == 'star_salmon' },
|
||||
fromState: [ "bam": "transcriptome_bam" ],
|
||||
toState: [ "transcriptome_bam": "output" ]
|
||||
)
|
||||
// Fix paired-end reads in name sorted BAM file
|
||||
| umi_tools_prepareforrsem.run (
|
||||
runIf: { id, state -> state.with_umi && state.paired && state.aligner == 'star_salmon' },
|
||||
fromState: [ "input": "transcriptome_bam" ],
|
||||
toState: [ "transcriptome_bam": "output" ]
|
||||
)
|
||||
|
||||
// Infer lib-type for salmon quant
|
||||
| map { id, state ->
|
||||
@@ -1597,78 +1599,91 @@ workflow run_wf {
|
||||
]
|
||||
)
|
||||
|
||||
| map { id, state ->
|
||||
def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state
|
||||
[ id, mod_state ]
|
||||
}
|
||||
|
||||
| rsem_calculate_expression.run (
|
||||
runIf: { id, state -> state.aligner == 'star_rsem' },
|
||||
fromState: [
|
||||
"id": "id",
|
||||
"strandedness": "strandedness",
|
||||
"paired": "paired",
|
||||
"input": "input",
|
||||
"index": "rsem_index",
|
||||
"extra_args": "extra_rsem_calculate_expression_args"
|
||||
],
|
||||
toState: [
|
||||
"rsem_counts_gene": "counts_gene",
|
||||
"rsem_counts_transcripts": "counts_transcripts",
|
||||
"rsem_multiqc": "stat",
|
||||
"star_multiqc": "logs",
|
||||
"bam_star_rsem": "bam_star",
|
||||
"bam_genome_rsem": "bam_genome",
|
||||
"bam_transcript_rsem": "bam_transcript"
|
||||
]
|
||||
)
|
||||
|
||||
// RSEM_Star BAM
|
||||
| samtools_sort.run (
|
||||
runIf: { id, state -> state.aligner == 'star_rsem' },
|
||||
fromState: ["input": "bam_star_rsem"],
|
||||
toState: ["genome_bam_sorted": "output"],
|
||||
key: "genome_sorted"
|
||||
)
|
||||
| samtools_index.run (
|
||||
runIf: { id, state -> state.aligner == 'star_rsem' },
|
||||
fromState: [
|
||||
"input": "genome_bam_sorted",
|
||||
"csi": "bam_csi_index"
|
||||
],
|
||||
toState: [ "genome_bam_index": "output" ],
|
||||
key: "genome_sorted"
|
||||
)
|
||||
| samtools_stats.run (
|
||||
runIf: { id, state -> state.aligner == 'star_rsem' },
|
||||
fromState: [
|
||||
"input": "genome_bam_sorted",
|
||||
"bai": "genome_bam_index",
|
||||
"fasta": "fasta"
|
||||
],
|
||||
toState: [ "genome_bam_stats": "output" ],
|
||||
key: "genome_stats"
|
||||
)
|
||||
| samtools_flagstat.run (
|
||||
runIf: { id, state -> state.aligner == 'star_rsem' },
|
||||
fromState: [
|
||||
"bam": "genome_bam_sorted",
|
||||
"bai": "genome_bam_index",
|
||||
"fasta": "fasta"
|
||||
],
|
||||
toState: [ "genome_bam_flagstat": "output" ],
|
||||
key: "genome_flagstat"
|
||||
)
|
||||
| samtools_idxstats.run(
|
||||
runIf: { id, state -> state.aligner == 'star_rsem' },
|
||||
fromState: [
|
||||
"bam": "genome_bam_sorted",
|
||||
"bai": "genome_bam_index",
|
||||
"fasta": "fasta"
|
||||
],
|
||||
toState: [ "genome_bam_idxstats": "output" ],
|
||||
key: "genome_idxstats"
|
||||
)
|
||||
| map { id, state ->
|
||||
def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state
|
||||
[ id, mod_state ]
|
||||
}
|
||||
|
||||
| rsem_calculate_expression.run (
|
||||
runIf: { id, state -> state.aligner == 'star_rsem' },
|
||||
fromState: [
|
||||
"id": "id",
|
||||
"strandedness": "strandedness",
|
||||
"paired": "paired",
|
||||
"input": "input",
|
||||
"index": "rsem_index",
|
||||
"counts_gene": "rsem_counts_gene",
|
||||
"counts_transcripts": "rsem_counts_transcripts",
|
||||
"stat": "rsem_multiqc",
|
||||
"logs": "star_multiqc",
|
||||
"bam_star": "bam_star_rsem",
|
||||
"bam_genome": "bam_genome_rsem",
|
||||
"bam_transcript": "bam_transcript_rsem"
|
||||
],
|
||||
args: [
|
||||
star: true,
|
||||
star_output_genome_bam: true,
|
||||
star_gzipped_read_file: true,
|
||||
estimate_rspd: true,
|
||||
seed: 1
|
||||
],
|
||||
toState: [
|
||||
"rsem_counts_gene": "counts_gene",
|
||||
"rsem_counts_transcripts": "counts_transcripts",
|
||||
"rsem_multiqc": "stat",
|
||||
"star_multiqc": "logs",
|
||||
"bam_star_rsem": "bam_star",
|
||||
"bam_genome_rsem": "bam_genome",
|
||||
"bam_transcript_rsem": "bam_transcript"
|
||||
]
|
||||
)
|
||||
|
||||
// RSEM_Star BAM
|
||||
| samtools_sort.run (
|
||||
runIf: { id, state -> state.aligner == 'star_rsem' },
|
||||
fromState: ["input": "bam_star_rsem"],
|
||||
toState: ["genome_bam_sorted": "output"],
|
||||
key: "genome_sorted"
|
||||
)
|
||||
| samtools_index.run (
|
||||
runIf: { id, state -> state.aligner == 'star_rsem' },
|
||||
fromState: [
|
||||
"input": "genome_bam_sorted",
|
||||
"csi": "bam_csi_index"
|
||||
],
|
||||
toState: [ "genome_bam_index": "output" ],
|
||||
key: "genome_sorted"
|
||||
)
|
||||
| samtools_stats.run (
|
||||
runIf: { id, state -> state.aligner == 'star_rsem' },
|
||||
fromState: [
|
||||
"input": "genome_bam_sorted",
|
||||
"bai": "genome_bam_index",
|
||||
"fasta": "fasta"
|
||||
],
|
||||
toState: [ "genome_bam_stats": "output" ],
|
||||
key: "genome_stats"
|
||||
)
|
||||
| samtools_flagstat.run (
|
||||
runIf: { id, state -> state.aligner == 'star_rsem' },
|
||||
fromState: [
|
||||
"bam": "genome_bam_sorted",
|
||||
"bai": "genome_bam_index",
|
||||
"fasta": "fasta"
|
||||
],
|
||||
toState: [ "genome_bam_flagstat": "output" ],
|
||||
key: "genome_flagstat"
|
||||
)
|
||||
| samtools_idxstats.run(
|
||||
runIf: { id, state -> state.aligner == 'star_rsem' },
|
||||
fromState: [
|
||||
"bam": "genome_bam_sorted",
|
||||
"bai": "genome_bam_index",
|
||||
"fasta": "fasta"
|
||||
],
|
||||
toState: [ "genome_bam_idxstats": "output" ],
|
||||
key: "genome_idxstats"
|
||||
)
|
||||
|
||||
| map { id, state ->
|
||||
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
|
||||
|
||||
@@ -197,7 +197,7 @@ dependencies:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -278,8 +278,8 @@ build_info:
|
||||
output: "target/executable/workflows/merge_quant_results"
|
||||
executable: "target/executable/workflows/merge_quant_results/merge_quant_results"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/nextflow/tx2gene"
|
||||
- "target/nextflow/tximport"
|
||||
@@ -294,7 +294,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -124,17 +124,6 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_bedtools_args"
|
||||
description: "Extra arguments to pass to bedtools genomecov command in addition\
|
||||
\ to defaults defined by the pipeline."
|
||||
info: null
|
||||
default:
|
||||
- ""
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--bam_csi_index"
|
||||
description: "Create a CSI index for BAM files instead of the traditional BAI\
|
||||
@@ -368,34 +357,36 @@ dependencies:
|
||||
- name: "samtools/samtools_sort"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_index"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_stats"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_flagstat"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_idxstats"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "stringtie"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "bedtools_genomecov"
|
||||
- name: "bedtools/bedtools_genomecov"
|
||||
repository:
|
||||
type: "local"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "ucsc/bedclip"
|
||||
repository:
|
||||
type: "local"
|
||||
@@ -405,7 +396,7 @@ dependencies:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -486,8 +477,8 @@ build_info:
|
||||
output: "target/executable/workflows/post_processing"
|
||||
executable: "target/executable/workflows/post_processing/post_processing"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/nextflow/picard_markduplicates"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"
|
||||
@@ -496,7 +487,7 @@ build_info:
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats"
|
||||
- "target/nextflow/stringtie"
|
||||
- "target/nextflow/bedtools_genomecov"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/bedtools/bedtools_genomecov"
|
||||
- "target/nextflow/ucsc/bedclip"
|
||||
- "target/nextflow/ucsc/bedgraphtobigwig"
|
||||
package_config:
|
||||
@@ -509,7 +500,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -232,12 +232,6 @@ function ViashHelp {
|
||||
echo " Perform reference-guided de novo assembly of transcripts using"
|
||||
echo " StringTie, i.e. don't restrict to those in GTF file."
|
||||
echo ""
|
||||
echo " --extra_bedtools_args"
|
||||
echo " type: string"
|
||||
echo " default:"
|
||||
echo " Extra arguments to pass to bedtools genomecov command in addition to"
|
||||
echo " defaults defined by the pipeline."
|
||||
echo ""
|
||||
echo " --bam_csi_index"
|
||||
echo " type: boolean"
|
||||
echo " default: false"
|
||||
@@ -485,17 +479,6 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_STRINGTIE_IGNORE_GTF=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--extra_bedtools_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_BEDTOOLS_ARGS" ] && ViashError Bad arguments for option \'--extra_bedtools_args\': \'$VIASH_PAR_EXTRA_BEDTOOLS_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_BEDTOOLS_ARGS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_bedtools_args. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_bedtools_args=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_BEDTOOLS_ARGS" ] && ViashError Bad arguments for option \'--extra_bedtools_args=*\': \'$VIASH_PAR_EXTRA_BEDTOOLS_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_BEDTOOLS_ARGS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--bam_csi_index)
|
||||
[ -n "$VIASH_PAR_BAM_CSI_INDEX" ] && ViashError Bad arguments for option \'--bam_csi_index\': \'$VIASH_PAR_BAM_CSI_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_BAM_CSI_INDEX="$2"
|
||||
@@ -877,9 +860,6 @@ fi
|
||||
if [ -z ${VIASH_PAR_EXTRA_STRINGTIE_ARGS+x} ]; then
|
||||
VIASH_PAR_EXTRA_STRINGTIE_ARGS=""
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_EXTRA_BEDTOOLS_ARGS+x} ]; then
|
||||
VIASH_PAR_EXTRA_BEDTOOLS_ARGS=""
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_BAM_CSI_INDEX+x} ]; then
|
||||
VIASH_PAR_BAM_CSI_INDEX="false"
|
||||
fi
|
||||
@@ -1140,7 +1120,6 @@ fi
|
||||
# set dependency paths
|
||||
VIASH_DEP_PICARD_MARKDUPLICATES="$VIASH_META_RESOURCES_DIR/../../../nextflow/picard_markduplicates/main.nf"
|
||||
VIASH_DEP_STRINGTIE="$VIASH_META_RESOURCES_DIR/../../../nextflow/stringtie/main.nf"
|
||||
VIASH_DEP_BEDTOOLS_GENOMECOV="$VIASH_META_RESOURCES_DIR/../../../nextflow/bedtools_genomecov/main.nf"
|
||||
VIASH_DEP_UCSC_BEDCLIP="$VIASH_META_RESOURCES_DIR/../../../nextflow/ucsc/bedclip/main.nf"
|
||||
VIASH_DEP_UCSC_BEDGRAPHTOBIGWIG="$VIASH_META_RESOURCES_DIR/../../../nextflow/ucsc/bedgraphtobigwig/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf"
|
||||
@@ -1148,6 +1127,7 @@ VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf"
|
||||
VIASH_DEP_BEDTOOLS_BEDTOOLS_GENOMECOV="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/bedtools/bedtools_genomecov/main.nf"
|
||||
|
||||
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
||||
cat << VIASHEOF | eval $VIASH_CMD
|
||||
@@ -1250,18 +1230,35 @@ workflow run_wf {
|
||||
|
||||
// Genome-wide coverage with BEDTools
|
||||
|
||||
| bedtools_genomecov.run (
|
||||
runIf: { id, state -> !state.skip_bigwig },
|
||||
fromState: [
|
||||
"strandedness": "strandedness",
|
||||
"bam": "processed_genome_bam",
|
||||
"extra_bedtools_args": "extra_bedtools_args"
|
||||
],
|
||||
toState: [
|
||||
"bedgraph_forward": "bedgraph_forward",
|
||||
"bedgraph_reverse": "bedgraph_reverse"
|
||||
]
|
||||
)
|
||||
| bedtools_genomecov.run (
|
||||
runIf: { id, state -> !state.skip_bigwig },
|
||||
fromState: [
|
||||
"input_bam": "processed_genome_bam",
|
||||
],
|
||||
args: [
|
||||
split: true,
|
||||
du: true,
|
||||
bed_graph: true,
|
||||
strand: "+"
|
||||
],
|
||||
toState: [ "bedgraph_forward": "output" ],
|
||||
key: "bedtools_genomecov_forward"
|
||||
)
|
||||
|
||||
| bedtools_genomecov.run (
|
||||
runIf: { id, state -> !state.skip_bigwig },
|
||||
fromState: [
|
||||
"input_bam": "processed_genome_bam",
|
||||
],
|
||||
args: [
|
||||
split: true,
|
||||
du: true,
|
||||
bed_graph: true,
|
||||
strand: "-"
|
||||
],
|
||||
toState: [ "bedgraph_reverse": "output" ],
|
||||
key: "bedtools_genomecov_reverse"
|
||||
)
|
||||
|
||||
| bedclip.run (
|
||||
runIf: { id, state -> !state.skip_bigwig },
|
||||
|
||||
@@ -57,19 +57,6 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--bbsplit_fasta_list"
|
||||
description: "Path to comma-separated file containing a list of reference genomes\
|
||||
\ to filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must\
|
||||
\ be explicitly set to \"false\". The file should contain 2 (comma separated)\
|
||||
\ columns - short name and full path to reference genome(s)"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--ribo_database_manifest"
|
||||
description: "Text file containing paths to fasta files (one per line) that will\
|
||||
@@ -267,15 +254,6 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_trimgalore_args"
|
||||
description: "Extra arguments to pass to Trim Galore! command in addition to defaults\
|
||||
\ defined by the pipeline."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--min_trimmed_reads"
|
||||
description: "Minimum number of trimmed reads below which samples are removed\
|
||||
@@ -308,19 +286,6 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Alignment options"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--extra_salmon_quant_args"
|
||||
description: "Extra arguments to pass to salmon quant command in addition to defaults\
|
||||
\ defined by the pipeline."
|
||||
info: null
|
||||
default:
|
||||
- ""
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Read filtering options"
|
||||
arguments:
|
||||
- type: "boolean_true"
|
||||
@@ -333,19 +298,6 @@ argument_groups:
|
||||
description: "Enable the removal of reads derived from ribosomal RNA using SortMeRNA."
|
||||
info: null
|
||||
direction: "input"
|
||||
- name: "Other options"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--extra_fq_subsample_args"
|
||||
description: "Extra arguments to pass to fq subsample command in addition to defaults\
|
||||
\ defined by the pipeline."
|
||||
info: null
|
||||
default:
|
||||
- "--record-count 1000000 --seed 1"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
@@ -353,7 +305,7 @@ argument_groups:
|
||||
description: "Path to output directory"
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_1.fastq"
|
||||
- "${id}_r1.fastq.gz"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -365,7 +317,7 @@ argument_groups:
|
||||
description: "Path to output directory"
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_2.fastq"
|
||||
- "${id}_r2.fastq.gz"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -377,7 +329,7 @@ argument_groups:
|
||||
description: "FastQC HTML report for read 1."
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_1.fastqc.html"
|
||||
- "${id}_r1.fastqc.html"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -389,7 +341,7 @@ argument_groups:
|
||||
description: "FastQC HTML report for read 2."
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_2.fastqc.html"
|
||||
- "${id}_r2.fastqc.html"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -401,7 +353,7 @@ argument_groups:
|
||||
description: "FastQC report archive for read 1."
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_1.fastqc.zip"
|
||||
- "${id}_r1.fastqc.zip"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -413,7 +365,7 @@ argument_groups:
|
||||
description: "FastQC report archive for read 2."
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_2.fastqc.zip"
|
||||
- "${id}_r2.fastqc.zip"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -424,7 +376,7 @@ argument_groups:
|
||||
name: "--trim_log_1"
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_1.trimming_report.txt"
|
||||
- "${id}_r1.trimming_report.txt"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -435,7 +387,7 @@ argument_groups:
|
||||
name: "--trim_log_2"
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_2.trimming_report.txt"
|
||||
- "${id}_r2.trimming_report.txt"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -446,7 +398,7 @@ argument_groups:
|
||||
name: "--trim_html_1"
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_1.trimmed_fastqc.html"
|
||||
- "${id}_r1.trimmed_fastqc.html"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -457,7 +409,7 @@ argument_groups:
|
||||
name: "--trim_html_2"
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_2.trimmed_fastqc.html"
|
||||
- "${id}_r2.trimmed_fastqc.html"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -468,7 +420,7 @@ argument_groups:
|
||||
name: "--trim_zip_1"
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_1.trimmed_fastqc.zip"
|
||||
- "${id}_r1.trimmed_fastqc.zip"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -479,7 +431,7 @@ argument_groups:
|
||||
name: "--trim_zip_2"
|
||||
info: null
|
||||
default:
|
||||
- "$id.read_2.trimmed_fastqc.zip"
|
||||
- "${id}_r2.trimmed_fastqc.zip"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -558,41 +510,48 @@ requirements:
|
||||
dependencies:
|
||||
- name: "fastqc"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "umitools/umitools_extract"
|
||||
repository:
|
||||
type: "local"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "umi_tools/umi_tools_extract"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "trimgalore"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "bbmap_bbsplit"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "bbmap/bbmap_bbsplit"
|
||||
repository:
|
||||
type: "local"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "sortmerna"
|
||||
repository:
|
||||
type: "local"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "fastp"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "fq_subsample"
|
||||
repository:
|
||||
type: "local"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "salmon/salmon_quant"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -673,17 +632,16 @@ build_info:
|
||||
output: "target/executable/workflows/pre_processing"
|
||||
executable: "target/executable/workflows/pre_processing/pre_processing"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/nextflow/fastqc"
|
||||
- "target/nextflow/umitools/umitools_extract"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/fastqc"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract"
|
||||
- "target/nextflow/trimgalore"
|
||||
- "target/nextflow/bbmap_bbsplit"
|
||||
- "target/nextflow/sortmerna"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/trimgalore"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/bbmap/bbmap_bbsplit"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/sortmerna"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/fastp"
|
||||
- "target/nextflow/fq_subsample"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/fq_subsample"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
@@ -695,7 +653,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -200,13 +200,6 @@ function ViashHelp {
|
||||
echo " type: file, file must exist"
|
||||
echo " BBsplit index"
|
||||
echo ""
|
||||
echo " --bbsplit_fasta_list"
|
||||
echo " type: file, file must exist"
|
||||
echo " Path to comma-separated file containing a list of reference genomes to"
|
||||
echo " filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must"
|
||||
echo " be explicitly set to \"false\". The file should contain 2 (comma"
|
||||
echo " separated) columns - short name and full path to reference genome(s)"
|
||||
echo ""
|
||||
echo " --ribo_database_manifest"
|
||||
echo " type: file, file must exist"
|
||||
echo " Text file containing paths to fasta files (one per line) that will be"
|
||||
@@ -302,11 +295,6 @@ function ViashHelp {
|
||||
echo " choices: [ trimgalore, fastp ]"
|
||||
echo " Specify the trimming tool to use."
|
||||
echo ""
|
||||
echo " --extra_trimgalore_args"
|
||||
echo " type: string"
|
||||
echo " Extra arguments to pass to Trim Galore! command in addition to defaults"
|
||||
echo " defined by the pipeline."
|
||||
echo ""
|
||||
echo " --min_trimmed_reads"
|
||||
echo " type: integer"
|
||||
echo " default: 10000"
|
||||
@@ -324,13 +312,6 @@ function ViashHelp {
|
||||
echo " default: false"
|
||||
echo " Save the trimmed FastQ files in the results directory."
|
||||
echo ""
|
||||
echo "Alignment options:"
|
||||
echo " --extra_salmon_quant_args"
|
||||
echo " type: string"
|
||||
echo " default:"
|
||||
echo " Extra arguments to pass to salmon quant command in addition to defaults"
|
||||
echo " defined by the pipeline."
|
||||
echo ""
|
||||
echo "Read filtering options:"
|
||||
echo " --skip_bbsplit"
|
||||
echo " type: boolean_true"
|
||||
@@ -340,67 +321,60 @@ function ViashHelp {
|
||||
echo " type: boolean_true"
|
||||
echo " Enable the removal of reads derived from ribosomal RNA using SortMeRNA."
|
||||
echo ""
|
||||
echo "Other options:"
|
||||
echo " --extra_fq_subsample_args"
|
||||
echo " type: string"
|
||||
echo " default: --record-count 1000000 --seed 1"
|
||||
echo " Extra arguments to pass to fq subsample command in addition to defaults"
|
||||
echo " defined by the pipeline."
|
||||
echo ""
|
||||
echo "Output:"
|
||||
echo " --qc_output1"
|
||||
echo " type: file, output"
|
||||
echo " default: \$id.read_1.fastq"
|
||||
echo " default: \${id}_r1.fastq.gz"
|
||||
echo " Path to output directory"
|
||||
echo ""
|
||||
echo " --qc_output2"
|
||||
echo " type: file, output"
|
||||
echo " default: \$id.read_2.fastq"
|
||||
echo " default: \${id}_r2.fastq.gz"
|
||||
echo " Path to output directory"
|
||||
echo ""
|
||||
echo " --fastqc_html_1"
|
||||
echo " type: file, output"
|
||||
echo " default: \$id.read_1.fastqc.html"
|
||||
echo " default: \${id}_r1.fastqc.html"
|
||||
echo " FastQC HTML report for read 1."
|
||||
echo ""
|
||||
echo " --fastqc_html_2"
|
||||
echo " type: file, output"
|
||||
echo " default: \$id.read_2.fastqc.html"
|
||||
echo " default: \${id}_r2.fastqc.html"
|
||||
echo " FastQC HTML report for read 2."
|
||||
echo ""
|
||||
echo " --fastqc_zip_1"
|
||||
echo " type: file, output"
|
||||
echo " default: \$id.read_1.fastqc.zip"
|
||||
echo " default: \${id}_r1.fastqc.zip"
|
||||
echo " FastQC report archive for read 1."
|
||||
echo ""
|
||||
echo " --fastqc_zip_2"
|
||||
echo " type: file, output"
|
||||
echo " default: \$id.read_2.fastqc.zip"
|
||||
echo " default: \${id}_r2.fastqc.zip"
|
||||
echo " FastQC report archive for read 2."
|
||||
echo ""
|
||||
echo " --trim_log_1"
|
||||
echo " type: file, output"
|
||||
echo " default: \$id.read_1.trimming_report.txt"
|
||||
echo " default: \${id}_r1.trimming_report.txt"
|
||||
echo ""
|
||||
echo " --trim_log_2"
|
||||
echo " type: file, output"
|
||||
echo " default: \$id.read_2.trimming_report.txt"
|
||||
echo " default: \${id}_r2.trimming_report.txt"
|
||||
echo ""
|
||||
echo " --trim_html_1"
|
||||
echo " type: file, output"
|
||||
echo " default: \$id.read_1.trimmed_fastqc.html"
|
||||
echo " default: \${id}_r1.trimmed_fastqc.html"
|
||||
echo ""
|
||||
echo " --trim_html_2"
|
||||
echo " type: file, output"
|
||||
echo " default: \$id.read_2.trimmed_fastqc.html"
|
||||
echo " default: \${id}_r2.trimmed_fastqc.html"
|
||||
echo ""
|
||||
echo " --trim_zip_1"
|
||||
echo " type: file, output"
|
||||
echo " default: \$id.read_1.trimmed_fastqc.zip"
|
||||
echo " default: \${id}_r1.trimmed_fastqc.zip"
|
||||
echo ""
|
||||
echo " --trim_zip_2"
|
||||
echo " type: file, output"
|
||||
echo " default: \$id.read_2.trimmed_fastqc.zip"
|
||||
echo " default: \${id}_r2.trimmed_fastqc.zip"
|
||||
echo ""
|
||||
echo " --sortmerna_log"
|
||||
echo " type: file, output"
|
||||
@@ -511,17 +485,6 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_BBSPLIT_INDEX=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--bbsplit_fasta_list)
|
||||
[ -n "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && ViashError Bad arguments for option \'--bbsplit_fasta_list\': \'$VIASH_PAR_BBSPLIT_FASTA_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_BBSPLIT_FASTA_LIST="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bbsplit_fasta_list. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--bbsplit_fasta_list=*)
|
||||
[ -n "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && ViashError Bad arguments for option \'--bbsplit_fasta_list=*\': \'$VIASH_PAR_BBSPLIT_FASTA_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_BBSPLIT_FASTA_LIST=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--ribo_database_manifest)
|
||||
[ -n "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ] && ViashError Bad arguments for option \'--ribo_database_manifest\': \'$VIASH_PAR_RIBO_DATABASE_MANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_RIBO_DATABASE_MANIFEST="$2"
|
||||
@@ -709,17 +672,6 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_TRIMMER=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--extra_trimgalore_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_TRIMGALORE_ARGS" ] && ViashError Bad arguments for option \'--extra_trimgalore_args\': \'$VIASH_PAR_EXTRA_TRIMGALORE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_TRIMGALORE_ARGS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_trimgalore_args. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_trimgalore_args=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_TRIMGALORE_ARGS" ] && ViashError Bad arguments for option \'--extra_trimgalore_args=*\': \'$VIASH_PAR_EXTRA_TRIMGALORE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_TRIMGALORE_ARGS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--min_trimmed_reads)
|
||||
[ -n "$VIASH_PAR_MIN_TRIMMED_READS" ] && ViashError Bad arguments for option \'--min_trimmed_reads\': \'$VIASH_PAR_MIN_TRIMMED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_MIN_TRIMMED_READS="$2"
|
||||
@@ -753,17 +705,6 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_SAVE_TRIMMED=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--extra_salmon_quant_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS" ] && ViashError Bad arguments for option \'--extra_salmon_quant_args\': \'$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_SALMON_QUANT_ARGS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_salmon_quant_args. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_salmon_quant_args=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS" ] && ViashError Bad arguments for option \'--extra_salmon_quant_args=*\': \'$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_SALMON_QUANT_ARGS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--skip_bbsplit)
|
||||
[ -n "$VIASH_PAR_SKIP_BBSPLIT" ] && ViashError Bad arguments for option \'--skip_bbsplit\': \'$VIASH_PAR_SKIP_BBSPLIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_SKIP_BBSPLIT=true
|
||||
@@ -774,17 +715,6 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_REMOVE_RIBO_RNA=true
|
||||
shift 1
|
||||
;;
|
||||
--extra_fq_subsample_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS" ] && ViashError Bad arguments for option \'--extra_fq_subsample_args\': \'$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_fq_subsample_args. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_fq_subsample_args=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS" ] && ViashError Bad arguments for option \'--extra_fq_subsample_args=*\': \'$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--qc_output1)
|
||||
[ -n "$VIASH_PAR_QC_OUTPUT1" ] && ViashError Bad arguments for option \'--qc_output1\': \'$VIASH_PAR_QC_OUTPUT1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QC_OUTPUT1="$2"
|
||||
@@ -1154,53 +1084,47 @@ fi
|
||||
if [ -z ${VIASH_PAR_SAVE_TRIMMED+x} ]; then
|
||||
VIASH_PAR_SAVE_TRIMMED="false"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_EXTRA_SALMON_QUANT_ARGS+x} ]; then
|
||||
VIASH_PAR_EXTRA_SALMON_QUANT_ARGS=""
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_SKIP_BBSPLIT+x} ]; then
|
||||
VIASH_PAR_SKIP_BBSPLIT="false"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_REMOVE_RIBO_RNA+x} ]; then
|
||||
VIASH_PAR_REMOVE_RIBO_RNA="false"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS+x} ]; then
|
||||
VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS="--record-count 1000000 --seed 1"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_QC_OUTPUT1+x} ]; then
|
||||
VIASH_PAR_QC_OUTPUT1="\$id.read_1.fastq"
|
||||
VIASH_PAR_QC_OUTPUT1="\${id}_r1.fastq.gz"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_QC_OUTPUT2+x} ]; then
|
||||
VIASH_PAR_QC_OUTPUT2="\$id.read_2.fastq"
|
||||
VIASH_PAR_QC_OUTPUT2="\${id}_r2.fastq.gz"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_FASTQC_HTML_1+x} ]; then
|
||||
VIASH_PAR_FASTQC_HTML_1="\$id.read_1.fastqc.html"
|
||||
VIASH_PAR_FASTQC_HTML_1="\${id}_r1.fastqc.html"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_FASTQC_HTML_2+x} ]; then
|
||||
VIASH_PAR_FASTQC_HTML_2="\$id.read_2.fastqc.html"
|
||||
VIASH_PAR_FASTQC_HTML_2="\${id}_r2.fastqc.html"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_FASTQC_ZIP_1+x} ]; then
|
||||
VIASH_PAR_FASTQC_ZIP_1="\$id.read_1.fastqc.zip"
|
||||
VIASH_PAR_FASTQC_ZIP_1="\${id}_r1.fastqc.zip"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_FASTQC_ZIP_2+x} ]; then
|
||||
VIASH_PAR_FASTQC_ZIP_2="\$id.read_2.fastqc.zip"
|
||||
VIASH_PAR_FASTQC_ZIP_2="\${id}_r2.fastqc.zip"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_TRIM_LOG_1+x} ]; then
|
||||
VIASH_PAR_TRIM_LOG_1="\$id.read_1.trimming_report.txt"
|
||||
VIASH_PAR_TRIM_LOG_1="\${id}_r1.trimming_report.txt"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_TRIM_LOG_2+x} ]; then
|
||||
VIASH_PAR_TRIM_LOG_2="\$id.read_2.trimming_report.txt"
|
||||
VIASH_PAR_TRIM_LOG_2="\${id}_r2.trimming_report.txt"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_TRIM_HTML_1+x} ]; then
|
||||
VIASH_PAR_TRIM_HTML_1="\$id.read_1.trimmed_fastqc.html"
|
||||
VIASH_PAR_TRIM_HTML_1="\${id}_r1.trimmed_fastqc.html"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_TRIM_HTML_2+x} ]; then
|
||||
VIASH_PAR_TRIM_HTML_2="\$id.read_2.trimmed_fastqc.html"
|
||||
VIASH_PAR_TRIM_HTML_2="\${id}_r2.trimmed_fastqc.html"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_TRIM_ZIP_1+x} ]; then
|
||||
VIASH_PAR_TRIM_ZIP_1="\$id.read_1.trimmed_fastqc.zip"
|
||||
VIASH_PAR_TRIM_ZIP_1="\${id}_r1.trimmed_fastqc.zip"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_TRIM_ZIP_2+x} ]; then
|
||||
VIASH_PAR_TRIM_ZIP_2="\$id.read_2.trimmed_fastqc.zip"
|
||||
VIASH_PAR_TRIM_ZIP_2="\${id}_r2.trimmed_fastqc.zip"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_SORTMERNA_LOG+x} ]; then
|
||||
VIASH_PAR_SORTMERNA_LOG="\$id.sortmerna.log"
|
||||
@@ -1224,10 +1148,6 @@ if [ ! -z "$VIASH_PAR_BBSPLIT_INDEX" ] && [ ! -e "$VIASH_PAR_BBSPLIT_INDEX" ]; t
|
||||
ViashError "Input file '$VIASH_PAR_BBSPLIT_INDEX' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && [ ! -e "$VIASH_PAR_BBSPLIT_FASTA_LIST" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_BBSPLIT_FASTA_LIST' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ] && [ ! -e "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_RIBO_DATABASE_MANIFEST' does not exist."
|
||||
exit 1
|
||||
@@ -1504,14 +1424,13 @@ fi
|
||||
|
||||
|
||||
# set dependency paths
|
||||
VIASH_DEP_FASTQC="$VIASH_META_RESOURCES_DIR/../../../nextflow/fastqc/main.nf"
|
||||
VIASH_DEP_UMITOOLS_UMITOOLS_EXTRACT="$VIASH_META_RESOURCES_DIR/../../../nextflow/umitools/umitools_extract/main.nf"
|
||||
VIASH_DEP_TRIMGALORE="$VIASH_META_RESOURCES_DIR/../../../nextflow/trimgalore/main.nf"
|
||||
VIASH_DEP_BBMAP_BBSPLIT="$VIASH_META_RESOURCES_DIR/../../../nextflow/bbmap_bbsplit/main.nf"
|
||||
VIASH_DEP_SORTMERNA="$VIASH_META_RESOURCES_DIR/../../../nextflow/sortmerna/main.nf"
|
||||
VIASH_DEP_FQ_SUBSAMPLE="$VIASH_META_RESOURCES_DIR/../../../nextflow/fq_subsample/main.nf"
|
||||
VIASH_DEP_FASTQC="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/fastqc/main.nf"
|
||||
VIASH_DEP_UMI_TOOLS_UMI_TOOLS_EXTRACT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf"
|
||||
VIASH_DEP_TRIMGALORE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/trimgalore/main.nf"
|
||||
VIASH_DEP_BBMAP_BBMAP_BBSPLIT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/bbmap/bbmap_bbsplit/main.nf"
|
||||
VIASH_DEP_SORTMERNA="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/sortmerna/main.nf"
|
||||
VIASH_DEP_FASTP="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf"
|
||||
VIASH_DEP_FQ_SUBSAMPLE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/fq_subsample/main.nf"
|
||||
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf"
|
||||
|
||||
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
||||
@@ -1546,48 +1465,58 @@ workflow run_wf {
|
||||
[ id, state + [paired: paired, input: input] ]
|
||||
}
|
||||
|
||||
// Perform QC on input fastq files
|
||||
| fastqc.run (
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_fastqc },
|
||||
fromState: { id, state ->
|
||||
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
||||
[ paired: state.paired,
|
||||
input: input ]
|
||||
},
|
||||
toState: [
|
||||
"fastqc_html_1": "fastqc_html_1",
|
||||
"fastqc_html_2": "fastqc_html_2",
|
||||
"fastqc_zip_1": "fastqc_zip_1",
|
||||
"fastqc_zip_2": "fastqc_zip_2"
|
||||
]
|
||||
fromState: [ "input": "input" ],
|
||||
toState: {id, output_state, state ->
|
||||
def newKeys = [
|
||||
"fastqc_html_1":output_state["html"][0],
|
||||
"fastqc_html_2": output_state["html"][1],
|
||||
"fastqc_zip_1": output_state["zip"][0],
|
||||
"fastqc_zip_2": output_state["zip"][1]
|
||||
]
|
||||
def new_state = state + newKeys
|
||||
return new_state
|
||||
},
|
||||
args: [html: "*.html", zip: "*.zip"]
|
||||
)
|
||||
|
||||
// Extract UMIs from fastq files and discard read 1 or read 2 if required
|
||||
| umitools_extract.run (
|
||||
| umi_tools_extract.run (
|
||||
runIf: { id, state -> state.with_umi && !state.skip_umi_extract },
|
||||
fromState: { id, state ->
|
||||
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
||||
def bc_pattern = state.paired ? [ state.umitools_bc_pattern, state.umitools_bc_pattern2 ] : [ state.umitools_bc_pattern ]
|
||||
[ paired: state.paired,
|
||||
input: input,
|
||||
bc_pattern: bc_pattern,
|
||||
umi_discard_read: state.umi_discard_read ]
|
||||
def bc_pattern2 = state.paired ? state.umitools_bc_pattern2 : state.remove(state.umitools_bc_pattern2)
|
||||
def output = "\${id}.r1.fastq.gz"
|
||||
def read2_out = state.paired ? "\${id}.r2.fastq.gz" : state.remove(state.fastq_2)
|
||||
[ input: state.fastq_1,
|
||||
read2_in: state.fastq_2,
|
||||
bc_pattern: state.umitools_bc_pattern,
|
||||
bc_pattern2: bc_pattern2,
|
||||
extract_method: state.umitools_extract_method,
|
||||
umi_separator: state.umitools_umi_separator,
|
||||
grouping_method: state.umitools_grouping_method,
|
||||
output: output,
|
||||
read2_out: read2_out ]
|
||||
},
|
||||
toState: [
|
||||
"fastq_1": "fastq_1",
|
||||
"fastq_2": "fastq_2"
|
||||
"fastq_1": "output",
|
||||
"fastq_2": "read2_out"
|
||||
]
|
||||
)
|
||||
|
||||
// Discard read if required
|
||||
| map { id, state ->
|
||||
def paired = state.paired
|
||||
def fastq_1 = state.fastq_1
|
||||
def fastq_2 = state.fastq_2
|
||||
if (paired && state.with_umi && !state.skip_umi_extract && state.umi_discard_read != 0) {
|
||||
fastq_2 = state.remove(state.fastq_2)
|
||||
if (state.umi_discard_read == 1) {
|
||||
fastq_1 = fastq_2
|
||||
}
|
||||
fastq_2 = state.remove(state.fastq_2)
|
||||
paired = false
|
||||
}
|
||||
[ id, state + [paired: paired, fastq_2: fastq_2] ]
|
||||
[ id, state + [paired: paired, fastq_1: fastq_1, fastq_2: fastq_2] ]
|
||||
}
|
||||
|
||||
// Trim reads using Trim galore!
|
||||
@@ -1597,8 +1526,11 @@ workflow run_wf {
|
||||
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
||||
[ paired: state.paired,
|
||||
input: input,
|
||||
min_trimmed_reads: state.min_trimmed_reads ]
|
||||
min_trimmed_reads: state.min_trimmed_reads,
|
||||
trimmed_r1: state.qc_output1,
|
||||
trimmed_r2: state.qc_output2 ]
|
||||
},
|
||||
args: [gzip: true, fastqc: true],
|
||||
toState: [
|
||||
"fastq_1": "trimmed_r1",
|
||||
"fastq_2": "trimmed_r2",
|
||||
@@ -1608,21 +1540,22 @@ workflow run_wf {
|
||||
"trim_zip_2": "trimmed_fastqc_zip_2",
|
||||
"trim_html_1": "trimmed_fastqc_html_1",
|
||||
"trim_html_2": "trimmed_fastqc_html_2"
|
||||
],
|
||||
args: [gzip: true, fastqc: true]
|
||||
]
|
||||
)
|
||||
|
||||
// Trim reads using fastp
|
||||
| fastp.run(
|
||||
runIf: { id, state -> !state.skip_trimming && state.trimmer == "fastp" },
|
||||
fromState: [
|
||||
"in1": "fastq_1",
|
||||
"in2": "fastq_2",
|
||||
"merge": "fastp_save_merged",
|
||||
"interleaved_in": "interleaved_reads",
|
||||
"detect_adapter_for_pe": "fastp_pe_detect_adapter",
|
||||
"adapter_fasta": "fastp_adapter_fasta"
|
||||
],
|
||||
fromState: { id, state ->
|
||||
def outputState = state.paired ? [out1: state.qc_output1, out2: state.qc_output2] : [out1: state.qc_output1, out2: state.remove(state.qc_output2)]
|
||||
[input_1: state.fastq_1, input_2: state.fastq_2] + outputState
|
||||
[ in1: state.fastq_1,
|
||||
in2: state.fastq_2,
|
||||
merge: state.fastp_save_merged,
|
||||
interleaved_in: state.interleaved_reads,
|
||||
detect_adapter_for_pe: state.paired,
|
||||
adapter_fasta: state.fastp_adapter_fasta ] + outputState
|
||||
},
|
||||
toState: [
|
||||
"fastq_1": "out1",
|
||||
"fastq_2": "out2",
|
||||
@@ -1636,19 +1569,23 @@ workflow run_wf {
|
||||
)
|
||||
|
||||
// Perform FASTQC on reads trimmed using fastp
|
||||
| fastqc.run(
|
||||
| fastqc.run (
|
||||
runIf: { id, state -> !state.skip_trimming && state.trimmer == "fastp" },
|
||||
fromState: { id, state ->
|
||||
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
||||
[ paired: state.paired,
|
||||
input: input ]
|
||||
},
|
||||
toState: [
|
||||
"trim_html_1": "fastqc_html_1",
|
||||
"trim_html_2": "fastqc_html_2",
|
||||
"trim_zip_1": "fastqc_zip_1",
|
||||
"trim_zip_2": "fastqc_zip_2"
|
||||
],
|
||||
[ input: input ]
|
||||
},
|
||||
toState: {id, output_state, state ->
|
||||
def newKeys = [
|
||||
"trim_html_1":output_state["html"][0],
|
||||
"trim_html_2": output_state["html"][1],
|
||||
"trim_zip_1": output_state["zip"][0],
|
||||
"trim_zip_2": output_state["zip"][1]
|
||||
]
|
||||
def new_state = state + newKeys
|
||||
return new_state
|
||||
},
|
||||
args: [html: "*.html", zip: "*.zip"],
|
||||
key: "fastqc_trimming"
|
||||
)
|
||||
|
||||
@@ -1659,7 +1596,7 @@ workflow run_wf {
|
||||
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
||||
[ paired: state.paired,
|
||||
input: input,
|
||||
built_bbsplit_index: state.bbsplit_index ]
|
||||
build: state.bbsplit_index ]
|
||||
},
|
||||
args: ["only_build_index": false],
|
||||
toState: [
|
||||
@@ -1675,27 +1612,44 @@ workflow run_wf {
|
||||
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
||||
def filePaths = state.ribo_database_manifest.readLines()
|
||||
def refs = filePaths.collect { it }
|
||||
[ paired: state.paired,
|
||||
def other = "\${id}_non_rRNA_reads/"
|
||||
[ paired_in: state.paired,
|
||||
input: input,
|
||||
ribo_database_manifest: refs ]
|
||||
ref: refs,
|
||||
out2: state.paired,
|
||||
other: other ]
|
||||
},
|
||||
toState: [
|
||||
"fastq_1": "fastq_1",
|
||||
"fastq_2": "fastq_2",
|
||||
"sortmerna_log": "sortmerna_log"
|
||||
]
|
||||
args: [fastx: true, num_alignments: 1],
|
||||
toState: { id, output_state, state ->
|
||||
def newKeys = [
|
||||
"sortmerna_output": output_state["other"],
|
||||
"sortmerna_log": output_state["log"]
|
||||
]
|
||||
def new_state = state + newKeys
|
||||
return new_state
|
||||
}
|
||||
)
|
||||
| map { id, state ->
|
||||
if (state.remove_ribo_rna) {
|
||||
def fastq_1 = state.sortmerna_output.listFiles().find{it.name == "other_fwd.fq.gz"}
|
||||
def fastq_2 = state.sortmerna_output.listFiles().find{it.name == "other_rev.fq.gz"}
|
||||
[ id, state + [fastq_1: fastq_1, fastq_2: fastq_2] ]
|
||||
} else {
|
||||
[ id, state ]
|
||||
}
|
||||
}
|
||||
|
||||
// Sub-sample FastQ files and pseudo-align with Salmon to auto-infer strandedness
|
||||
| fq_subsample.run (
|
||||
runIf: { id, state -> state.strandedness == 'auto' },
|
||||
fromState: { id, state ->
|
||||
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
||||
[
|
||||
input: input,
|
||||
extra_args: state.extra_fq_subsample_args
|
||||
]
|
||||
fromState: { id, state ->
|
||||
def outputState = state.paired ? [output_1: state.qc_output1, output_2: state.qc_output2] : [output_1: state.qc_output1, output_2: state.remove(state.qc_output2)]
|
||||
[input_1: state.fastq_1, input_2: state.fastq_2] + outputState
|
||||
},
|
||||
args: [
|
||||
record_count: 1000,
|
||||
seed: 1
|
||||
],
|
||||
toState: [
|
||||
"subsampled_fastq_1": "output_1",
|
||||
"subsampled_fastq_2": "output_2"
|
||||
@@ -1721,6 +1675,7 @@ workflow run_wf {
|
||||
)
|
||||
[ id, state + [lib_type: lib_type] ]
|
||||
}
|
||||
|
||||
| salmon_quant.run (
|
||||
runIf: { id, state -> state.strandedness == 'auto' },
|
||||
fromState: { id, state ->
|
||||
@@ -1738,17 +1693,17 @@ workflow run_wf {
|
||||
toState: [ "salmon_quant_output": "output" ]
|
||||
)
|
||||
|
||||
| map { id, state ->
|
||||
def mod_state = (!state.paired) ?
|
||||
[trim_log_2: state.remove(state.trim_log_2), trim_zip_2: state.remove(state.trim_zip_2), trim_html_2: state.remove(state.trim_html_2), failed_trim_unpaired2: state.remove(state.failed_trim_unpaired2)] :
|
||||
[]
|
||||
[ id, state + mod_state ]
|
||||
}
|
||||
| map { id, state ->
|
||||
def mod_state = (!state.paired) ?
|
||||
[trim_log_2: state.remove(state.trim_log_2), trim_zip_2: state.remove(state.trim_zip_2), trim_html_2: state.remove(state.trim_html_2), failed_trim_unpaired2: state.remove(state.failed_trim_unpaired2)] :
|
||||
[]
|
||||
[ id, state + mod_state ]
|
||||
}
|
||||
|
||||
| map { id, state ->
|
||||
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
|
||||
[ id, mod_state ]
|
||||
}
|
||||
| map { id, state ->
|
||||
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
|
||||
[ id, mod_state ]
|
||||
}
|
||||
|
||||
| setState (
|
||||
"fastqc_html_1": "fastqc_html_1",
|
||||
@@ -1764,9 +1719,6 @@ workflow run_wf {
|
||||
"trim_html_1": "trim_html_1",
|
||||
"trim_html_2": "trim_html_2",
|
||||
"sortmerna_log": "sortmerna_log",
|
||||
"failed_trim": "failed_trim",
|
||||
"failed_trim_unpaired1": "failed_trim_unpaired1",
|
||||
"failed_trim_unpaired2": "failed_trim_unpaired2",
|
||||
"trim_json": "trim_json",
|
||||
"trim_html": "trim_html",
|
||||
"trim_merged_out": "trim_merged_out",
|
||||
|
||||
@@ -87,16 +87,14 @@ argument_groups:
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--bbsplit_fasta_list"
|
||||
description: "Path to comma-separated file containing a list of reference genomes\
|
||||
\ to filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must\
|
||||
\ be explicitly set to \"false\". The file should contain 2 (comma separated)\
|
||||
\ columns - short name and full path to reference genome(s)"
|
||||
description: "List of reference genomes (separated by \";\") to filter reads against\
|
||||
\ with BBSplit."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--star_index"
|
||||
@@ -126,15 +124,6 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "extra_rsem_prepare_reference_args"
|
||||
description: "Extra arguments to pass to rsem-prepare-reference command in addition\
|
||||
\ to defaults defined by the pipeline."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--salmon_index"
|
||||
description: "Path to directory or tar.gz archive for pre-built Salmon index."
|
||||
@@ -382,7 +371,7 @@ dependencies:
|
||||
- name: "gffread"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "cat_additional_fasta"
|
||||
repository:
|
||||
@@ -399,7 +388,7 @@ dependencies:
|
||||
- name: "rsem/rsem_prepare_reference"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "getchromsizes"
|
||||
repository:
|
||||
@@ -412,23 +401,27 @@ dependencies:
|
||||
- name: "star/star_genome_generate"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "bbmap_bbsplit"
|
||||
- name: "bbmap/bbmap_bbsplit"
|
||||
repository:
|
||||
type: "local"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "salmon/salmon_index"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "kallisto/kallisto_index"
|
||||
repository:
|
||||
type: "local"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -509,8 +502,8 @@ build_info:
|
||||
output: "target/executable/workflows/prepare_genome"
|
||||
executable: "target/executable/workflows/prepare_genome/prepare_genome"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/nextflow/gunzip"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread"
|
||||
@@ -522,9 +515,9 @@ build_info:
|
||||
- "target/nextflow/getchromsizes"
|
||||
- "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/untar"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate"
|
||||
- "target/nextflow/bbmap_bbsplit"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/bbmap/bbmap_bbsplit"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index"
|
||||
- "target/nextflow/kallisto/kallisto_index"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_index"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -535,7 +528,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -212,11 +212,9 @@ function ViashHelp {
|
||||
echo " Skip BBSplit for removal of non-reference genome reads."
|
||||
echo ""
|
||||
echo " --bbsplit_fasta_list"
|
||||
echo " type: file, file must exist"
|
||||
echo " Path to comma-separated file containing a list of reference genomes to"
|
||||
echo " filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must"
|
||||
echo " be explicitly set to \"false\". The file should contain 2 (comma"
|
||||
echo " separated) columns - short name and full path to reference genome(s)"
|
||||
echo " type: file, multiple values allowed, file must exist"
|
||||
echo " List of reference genomes (separated by \";\") to filter reads against"
|
||||
echo " with BBSplit."
|
||||
echo ""
|
||||
echo " --star_index"
|
||||
echo " type: file, file must exist"
|
||||
@@ -230,11 +228,6 @@ function ViashHelp {
|
||||
echo " type: file, file must exist"
|
||||
echo " Path to directory or tar.gz archive for pre-built RSEM index."
|
||||
echo ""
|
||||
echo " extra_rsem_prepare_reference_args"
|
||||
echo " type: string"
|
||||
echo " Extra arguments to pass to rsem-prepare-reference command in addition to"
|
||||
echo " defaults defined by the pipeline."
|
||||
echo ""
|
||||
echo " --salmon_index"
|
||||
echo " type: file, file must exist"
|
||||
echo " Path to directory or tar.gz archive for pre-built Salmon index."
|
||||
@@ -454,14 +447,20 @@ while [[ $# -gt 0 ]]; do
|
||||
shift 1
|
||||
;;
|
||||
--bbsplit_fasta_list)
|
||||
[ -n "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && ViashError Bad arguments for option \'--bbsplit_fasta_list\': \'$VIASH_PAR_BBSPLIT_FASTA_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_BBSPLIT_FASTA_LIST="$2"
|
||||
if [ -z "$VIASH_PAR_BBSPLIT_FASTA_LIST" ]; then
|
||||
VIASH_PAR_BBSPLIT_FASTA_LIST="$2"
|
||||
else
|
||||
VIASH_PAR_BBSPLIT_FASTA_LIST="$VIASH_PAR_BBSPLIT_FASTA_LIST;""$2"
|
||||
fi
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bbsplit_fasta_list. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--bbsplit_fasta_list=*)
|
||||
[ -n "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && ViashError Bad arguments for option \'--bbsplit_fasta_list=*\': \'$VIASH_PAR_BBSPLIT_FASTA_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_BBSPLIT_FASTA_LIST=$(ViashRemoveFlags "$1")
|
||||
if [ -z "$VIASH_PAR_BBSPLIT_FASTA_LIST" ]; then
|
||||
VIASH_PAR_BBSPLIT_FASTA_LIST=$(ViashRemoveFlags "$1")
|
||||
else
|
||||
VIASH_PAR_BBSPLIT_FASTA_LIST="$VIASH_PAR_BBSPLIT_FASTA_LIST;"$(ViashRemoveFlags "$1")
|
||||
fi
|
||||
shift 1
|
||||
;;
|
||||
--star_index)
|
||||
@@ -824,12 +823,6 @@ if [ -z "$VIASH_META_CPUS" ]; then
|
||||
fi
|
||||
|
||||
|
||||
# storing leftover values in positionals
|
||||
if [[ $# -gt 0 ]]; then
|
||||
VIASH_PAR_EXTRA_RSEM_PREPARE_REFERENCE_ARGS="$1"
|
||||
shift 1
|
||||
fi
|
||||
|
||||
# check whether required parameters exist
|
||||
if [ -z ${VIASH_PAR_FASTA+x} ]; then
|
||||
ViashError '--fasta' is a required argument. Use "--help" to get more information on the parameters.
|
||||
@@ -936,9 +929,17 @@ if [ ! -z "$VIASH_PAR_SPLICESITES" ] && [ ! -e "$VIASH_PAR_SPLICESITES" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_SPLICESITES' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && [ ! -e "$VIASH_PAR_BBSPLIT_FASTA_LIST" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_BBSPLIT_FASTA_LIST' does not exist."
|
||||
exit 1
|
||||
if [ ! -z "$VIASH_PAR_BBSPLIT_FASTA_LIST" ]; then
|
||||
IFS=';'
|
||||
set -f
|
||||
for file in $VIASH_PAR_BBSPLIT_FASTA_LIST; do
|
||||
unset IFS
|
||||
if [ ! -e "$file" ]; then
|
||||
ViashError "Input file '$file' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
done
|
||||
set +f
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_STAR_INDEX" ] && [ ! -e "$VIASH_PAR_STAR_INDEX" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_STAR_INDEX' does not exist."
|
||||
@@ -1142,13 +1143,13 @@ VIASH_DEP_GTF2BED="$VIASH_META_RESOURCES_DIR/../../../nextflow/gtf2bed/main.nf"
|
||||
VIASH_DEP_PREPROCESS_TRANSCRIPTS_FASTA="$VIASH_META_RESOURCES_DIR/../../../nextflow/preprocess_transcripts_fasta/main.nf"
|
||||
VIASH_DEP_GTF_FILTER="$VIASH_META_RESOURCES_DIR/../../../nextflow/gtf_filter/main.nf"
|
||||
VIASH_DEP_GETCHROMSIZES="$VIASH_META_RESOURCES_DIR/../../../nextflow/getchromsizes/main.nf"
|
||||
VIASH_DEP_BBMAP_BBSPLIT="$VIASH_META_RESOURCES_DIR/../../../nextflow/bbmap_bbsplit/main.nf"
|
||||
VIASH_DEP_KALLISTO_KALLISTO_INDEX="$VIASH_META_RESOURCES_DIR/../../../nextflow/kallisto/kallisto_index/main.nf"
|
||||
VIASH_DEP_GFFREAD="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf"
|
||||
VIASH_DEP_RSEM_RSEM_PREPARE_REFERENCE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf"
|
||||
VIASH_DEP_UNTAR="$VIASH_TARGET_DIR/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/untar/main.nf"
|
||||
VIASH_DEP_STAR_STAR_GENOME_GENERATE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf"
|
||||
VIASH_DEP_BBMAP_BBMAP_BBSPLIT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/bbmap/bbmap_bbsplit/main.nf"
|
||||
VIASH_DEP_SALMON_SALMON_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf"
|
||||
VIASH_DEP_KALLISTO_KALLISTO_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_index/main.nf"
|
||||
|
||||
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
||||
cat << VIASHEOF | eval $VIASH_CMD
|
||||
@@ -1308,43 +1309,45 @@ workflow run_wf {
|
||||
[ id, state + [transcript_fasta: transcript_fasta] ]
|
||||
}
|
||||
|
||||
// chromosome size and fai index
|
||||
| getchromsizes.run (
|
||||
fromState: [ "fasta": "fasta" ],
|
||||
toState: [
|
||||
"fai": "fai",
|
||||
"sizes": "sizes"
|
||||
],
|
||||
key: "chromsizes",
|
||||
args: [
|
||||
fai: "genome_additional.fasta.fai",
|
||||
sizes: "genome_additional.fasta.sizes"
|
||||
]
|
||||
)
|
||||
|
||||
// untar bbsplit index, if available
|
||||
| untar.run (
|
||||
runIf: {id, state -> state.bbsplit_index},
|
||||
fromState: [ "input": "bbsplit_index" ],
|
||||
toState: [ "bbsplit_index": "output" ],
|
||||
key: "untar_bbsplit_index",
|
||||
args: [output: "BBSplit_index"]
|
||||
)
|
||||
|
||||
// create bbsplit index, if not already availble
|
||||
| bbmap_bbsplit.run (
|
||||
runIf: {id, state -> !state.skip_bbsplit && !state.bbsplit_index},
|
||||
fromState: [
|
||||
"primary_ref": "fasta",
|
||||
"bbsplit_fasta_list": "bbsplit_fasta_list"
|
||||
],
|
||||
toState: [ "bbsplit_index": "bbsplit_index" ],
|
||||
args: [
|
||||
only_build_index: true,
|
||||
bbsplit_index: "BBSplit_index"
|
||||
],
|
||||
key: "generate_bbsplit_index"
|
||||
)
|
||||
// chromosome size and fai index
|
||||
| getchromsizes.run (
|
||||
fromState: [ "fasta": "fasta" ],
|
||||
toState: [
|
||||
"fai": "fai",
|
||||
"sizes": "sizes"
|
||||
],
|
||||
key: "chromsizes",
|
||||
args: [
|
||||
fai: "genome_additional.fasta.fai",
|
||||
sizes: "genome_additional.fasta.sizes"
|
||||
]
|
||||
)
|
||||
|
||||
// untar bbsplit index, if available
|
||||
| untar.run (
|
||||
runIf: {id, state -> state.bbsplit_index},
|
||||
fromState: [ "input": "bbsplit_index" ],
|
||||
toState: [ "bbsplit_index": "output" ],
|
||||
key: "untar_bbsplit_index",
|
||||
args: [output: "BBSplit_index"]
|
||||
)
|
||||
|
||||
| map {id, state ->
|
||||
def ref = [state.fasta] + state.bbsplit_fasta_list
|
||||
[id, state + [bbsplit_ref: ref] ]
|
||||
}
|
||||
|
||||
// create bbsplit index, if not already availble
|
||||
| bbmap_bbsplit.run (
|
||||
runIf: {id, state -> !state.skip_bbsplit && !state.bbsplit_index},
|
||||
fromState: ["ref": "bbsplit_ref"],
|
||||
toState: [ "bbsplit_index": "index" ],
|
||||
args: [
|
||||
only_build_index: true,
|
||||
index: "BBSplit_index"
|
||||
],
|
||||
key: "generate_bbsplit_index"
|
||||
)
|
||||
|
||||
// Uncompress STAR index or generate from scratch if required
|
||||
| untar.run (
|
||||
@@ -1421,16 +1424,16 @@ workflow run_wf {
|
||||
args: [output: "Kallisto_index"]
|
||||
)
|
||||
|
||||
| kallisto_index.run(
|
||||
runIf: {id, state -> state.pseudo_aligner == "kallisto" && !state.kallisto_index},
|
||||
fromState: [
|
||||
"transcriptome_fasta": "transcript_fasta",
|
||||
"pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size"
|
||||
],
|
||||
toState: [ "kallisto_index": "kallisto_index" ],
|
||||
key: "generate_kallisto_index",
|
||||
args: [kallisto_index: "Kallisto_index"]
|
||||
)
|
||||
| kallisto_index.run(
|
||||
runIf: {id, state -> state.pseudo_aligner == "kallisto" && !state.kallisto_index},
|
||||
fromState: [
|
||||
"input": "transcript_fasta",
|
||||
"kmer_size": "pseudo_aligner_kmer_size"
|
||||
],
|
||||
toState: [ "kallisto_index": "index" ],
|
||||
key: "generate_kallisto_index",
|
||||
args: [index: "Kallisto_index"]
|
||||
)
|
||||
|
||||
| map { id, state ->
|
||||
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
|
||||
|
||||
@@ -116,7 +116,7 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
- type: "double"
|
||||
name: "--kallisto_quant_fragment_length"
|
||||
description: "For single-end mode only, the estimated average fragment length\
|
||||
\ to use for quantification with Kallisto."
|
||||
@@ -125,7 +125,7 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
- type: "double"
|
||||
name: "--kallisto_quant_fragment_length_sd"
|
||||
description: "For single-end mode only, the estimated standard deviation of the\
|
||||
\ fragment length for quantification with Kallisto."
|
||||
@@ -194,15 +194,17 @@ dependencies:
|
||||
- name: "salmon/salmon_quant"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "kallisto/kallisto_quant"
|
||||
repository:
|
||||
type: "local"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -283,11 +285,11 @@ build_info:
|
||||
output: "target/executable/workflows/pseudo_alignment_and_quant"
|
||||
executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
|
||||
- "target/nextflow/kallisto/kallisto_quant"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_quant"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "main"
|
||||
@@ -298,7 +300,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -227,12 +227,12 @@ function ViashHelp {
|
||||
echo " object"
|
||||
echo ""
|
||||
echo " --kallisto_quant_fragment_length"
|
||||
echo " type: integer"
|
||||
echo " type: double"
|
||||
echo " For single-end mode only, the estimated average fragment length to use"
|
||||
echo " for quantification with Kallisto."
|
||||
echo ""
|
||||
echo " --kallisto_quant_fragment_length_sd"
|
||||
echo " type: integer"
|
||||
echo " type: double"
|
||||
echo " For single-end mode only, the estimated standard deviation of the"
|
||||
echo " fragment length for quantification with Kallisto."
|
||||
echo ""
|
||||
@@ -645,14 +645,14 @@ fi
|
||||
|
||||
# check whether parameters values are of the right type
|
||||
if [[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" ]]; then
|
||||
if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
|
||||
ViashError '--kallisto_quant_fragment_length' has to be an integer. Use "--help" to get more information on the parameters.
|
||||
if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
||||
ViashError '--kallisto_quant_fragment_length' has to be a double. Use "--help" to get more information on the parameters.
|
||||
exit 1
|
||||
fi
|
||||
fi
|
||||
if [[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" ]]; then
|
||||
if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" =~ ^[-+]?[0-9]+$ ]]; then
|
||||
ViashError '--kallisto_quant_fragment_length_sd' has to be an integer. Use "--help" to get more information on the parameters.
|
||||
if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
||||
ViashError '--kallisto_quant_fragment_length_sd' has to be a double. Use "--help" to get more information on the parameters.
|
||||
exit 1
|
||||
fi
|
||||
fi
|
||||
@@ -779,8 +779,8 @@ fi
|
||||
|
||||
|
||||
# set dependency paths
|
||||
VIASH_DEP_KALLISTO_KALLISTO_QUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/kallisto/kallisto_quant/main.nf"
|
||||
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf"
|
||||
VIASH_DEP_KALLISTO_KALLISTO_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_quant/main.nf"
|
||||
|
||||
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
||||
cat << VIASHEOF | eval $VIASH_CMD
|
||||
@@ -859,22 +859,32 @@ workflow run_wf {
|
||||
[ id, mod_state ]
|
||||
}
|
||||
|
||||
| kallisto_quant.run (
|
||||
runIf: { id, state -> state.pseudo_aligner == 'kallisto'},
|
||||
fromState: [
|
||||
"input": "input",
|
||||
"paired": "paired",
|
||||
"gtf": "gtf",
|
||||
"index": "kallisto_index",
|
||||
"fragment_length": "kallisto_quant_fragment_length",
|
||||
"fragment_length_sd": "kallisto_quant_fragment_length_sd"
|
||||
],
|
||||
toState: [
|
||||
"quant_out_dir": "output",
|
||||
"kallisto_quant_results_file": "quant_results_file",
|
||||
"pseudo_multiqc": "log"
|
||||
| kallisto_quant.run (
|
||||
runIf: { id, state -> state.pseudo_aligner == 'kallisto'},
|
||||
fromState: { id, state ->
|
||||
def fr_stranded = state.strandedness == 'forward'
|
||||
def rf_stranded = state.strandedness == 'reverse'
|
||||
[
|
||||
input: state.input,
|
||||
index: state.kallisto_index,
|
||||
fragment_length: state.kallisto_quant_fragment_length,
|
||||
sd: state.kallisto_quant_fragment_length_sd,
|
||||
single: !state.paired,
|
||||
fr_stranded: fr_stranded,
|
||||
rf_stranded: rf_stranded,
|
||||
]
|
||||
)
|
||||
},
|
||||
args: [log: "kallisto_quant.log"],
|
||||
toState: { id, output_state, state ->
|
||||
def neKeys = [
|
||||
"quant_out_dir": output_state["output_dir"],
|
||||
"kallisto_quant_results_file": output_state["output_dir"] + "/abundance.tsv",
|
||||
"pseudo_multiqc": output_state["log"]
|
||||
]
|
||||
def new_state = state + newKeys
|
||||
return new_state
|
||||
}
|
||||
)
|
||||
|
||||
| map { id, state ->
|
||||
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
|
||||
|
||||
@@ -281,15 +281,6 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_featurecounts_args"
|
||||
description: "Extra arguments to pass to featureCounts command in addition to\
|
||||
\ defaults defined by the pipeline"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--rseqc_modules"
|
||||
description: "Specify the RSeQC modules to run_wf"
|
||||
@@ -472,19 +463,6 @@ argument_groups:
|
||||
\ to determine tin. Only use this option if there are substantial intronic reads."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "string"
|
||||
name: "--output_format"
|
||||
description: "Format of the qualimap output report (PDF or HTML, default is HTML)"
|
||||
info: null
|
||||
default:
|
||||
- "html"
|
||||
required: false
|
||||
choices:
|
||||
- "html"
|
||||
- "pdf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--pr_bases"
|
||||
description: "Number of upstream/downstream nucleotide bases to compute 5'-3'\
|
||||
@@ -1127,21 +1105,33 @@ argument_groups:
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--qualimap_output_pdf"
|
||||
name: "--qualimap_qc_report"
|
||||
description: "Text file containing the RNAseq QC results."
|
||||
info: null
|
||||
default:
|
||||
- "$id.qualimap_output.pdf"
|
||||
must_exist: false
|
||||
example:
|
||||
- "$id.rnaseq_qc_results.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--qualimap_output_dir"
|
||||
name: "--qualimap_counts"
|
||||
description: "Output file for computed counts."
|
||||
info: null
|
||||
default:
|
||||
- "$id.qualimap_output"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--qualimap_report"
|
||||
description: "Report output file. Supported formats are PDF or HTML."
|
||||
info: null
|
||||
example:
|
||||
- "$id.report.html"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -1416,13 +1406,19 @@ requirements:
|
||||
dependencies:
|
||||
- name: "rseqc/rseqc_bamstat"
|
||||
repository:
|
||||
type: "local"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "rseqc/rseqc_inferexperiment"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "rseqc/rseqc_innerdistance"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "rseqc/rseqc_inner_distance"
|
||||
repository:
|
||||
type: "local"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "rseqc/rseqc_junctionannotation"
|
||||
repository:
|
||||
type: "local"
|
||||
@@ -1441,16 +1437,18 @@ dependencies:
|
||||
- name: "dupradar"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "qualimap"
|
||||
- name: "qualimap/qualimap_rnaseq"
|
||||
repository:
|
||||
type: "local"
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "preseq_lcextrap"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "featurecounts"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "multiqc_custom_biotype"
|
||||
repository:
|
||||
@@ -1464,9 +1462,9 @@ dependencies:
|
||||
- name: "multiqc"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- name: "rsem/rsem_merge_counts"
|
||||
- name: "rsem_merge_counts"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "workflows/merge_quant_results"
|
||||
@@ -1475,7 +1473,7 @@ dependencies:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -1556,26 +1554,26 @@ build_info:
|
||||
output: "target/executable/workflows/quality_control"
|
||||
executable: "target/executable/workflows/quality_control/quality_control"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/nextflow/rseqc/rseqc_bamstat"
|
||||
- "target/nextflow/rseqc/rseqc_inferexperiment"
|
||||
- "target/nextflow/rseqc/rseqc_innerdistance"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_bamstat"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inferexperiment"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inner_distance"
|
||||
- "target/nextflow/rseqc/rseqc_junctionannotation"
|
||||
- "target/nextflow/rseqc/rseqc_junctionsaturation"
|
||||
- "target/nextflow/rseqc/rseqc_readdistribution"
|
||||
- "target/nextflow/rseqc/rseqc_readduplication"
|
||||
- "target/nextflow/rseqc/rseqc_tin"
|
||||
- "target/nextflow/dupradar"
|
||||
- "target/nextflow/qualimap"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/qualimap/qualimap_rnaseq"
|
||||
- "target/nextflow/preseq_lcextrap"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts"
|
||||
- "target/nextflow/multiqc_custom_biotype"
|
||||
- "target/nextflow/deseq2_qc"
|
||||
- "target/nextflow/prepare_multiqc_input"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc"
|
||||
- "target/nextflow/rsem/rsem_merge_counts"
|
||||
- "target/nextflow/rsem_merge_counts"
|
||||
- "target/nextflow/workflows/merge_quant_results"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
@@ -1587,7 +1585,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -313,11 +313,6 @@ function ViashHelp {
|
||||
echo " Biotype value to use while appending entries to GTF file when additional"
|
||||
echo " fasta file is provided."
|
||||
echo ""
|
||||
echo " --extra_featurecounts_args"
|
||||
echo " type: string"
|
||||
echo " Extra arguments to pass to featureCounts command in addition to defaults"
|
||||
echo " defined by the pipeline"
|
||||
echo ""
|
||||
echo " --rseqc_modules"
|
||||
echo " type: string, multiple values allowed"
|
||||
echo " default:"
|
||||
@@ -424,12 +419,6 @@ function ViashHelp {
|
||||
echo " determine tin. Only use this option if there are substantial intronic"
|
||||
echo " reads."
|
||||
echo ""
|
||||
echo " --output_format"
|
||||
echo " type: string"
|
||||
echo " default: html"
|
||||
echo " choices: [ html, pdf ]"
|
||||
echo " Format of the qualimap output report (PDF or HTML, default is HTML)"
|
||||
echo ""
|
||||
echo " --pr_bases"
|
||||
echo " type: integer"
|
||||
echo " default: 100"
|
||||
@@ -701,13 +690,19 @@ function ViashHelp {
|
||||
echo " type: file, output, file must exist"
|
||||
echo " default: \$id.intercept_slope.txt"
|
||||
echo ""
|
||||
echo " --qualimap_output_pdf"
|
||||
echo " type: file, output"
|
||||
echo " default: \$id.qualimap_output.pdf"
|
||||
echo ""
|
||||
echo " --qualimap_output_dir"
|
||||
echo " --qualimap_qc_report"
|
||||
echo " type: file, output, file must exist"
|
||||
echo " default: \$id.qualimap_output"
|
||||
echo " example: \$id.rnaseq_qc_results.txt"
|
||||
echo " Text file containing the RNAseq QC results."
|
||||
echo ""
|
||||
echo " --qualimap_counts"
|
||||
echo " type: file, output, file must exist"
|
||||
echo " Output file for computed counts."
|
||||
echo ""
|
||||
echo " --qualimap_report"
|
||||
echo " type: file, output, file must exist"
|
||||
echo " example: \$id.report.html"
|
||||
echo " Report output file. Supported formats are PDF or HTML."
|
||||
echo ""
|
||||
echo " --deseq2_output"
|
||||
echo " type: file, output, file must exist"
|
||||
@@ -1146,17 +1141,6 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_BIOTYPE=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--extra_featurecounts_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_FEATURECOUNTS_ARGS" ] && ViashError Bad arguments for option \'--extra_featurecounts_args\': \'$VIASH_PAR_EXTRA_FEATURECOUNTS_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_FEATURECOUNTS_ARGS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_featurecounts_args. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_featurecounts_args=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_FEATURECOUNTS_ARGS" ] && ViashError Bad arguments for option \'--extra_featurecounts_args=*\': \'$VIASH_PAR_EXTRA_FEATURECOUNTS_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_FEATURECOUNTS_ARGS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--rseqc_modules)
|
||||
if [ -z "$VIASH_PAR_RSEQC_MODULES" ]; then
|
||||
VIASH_PAR_RSEQC_MODULES="$2"
|
||||
@@ -1322,17 +1306,6 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_SUBTRACT_BACKGROUND=true
|
||||
shift 1
|
||||
;;
|
||||
--output_format)
|
||||
[ -n "$VIASH_PAR_OUTPUT_FORMAT" ] && ViashError Bad arguments for option \'--output_format\': \'$VIASH_PAR_OUTPUT_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_OUTPUT_FORMAT="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output_format. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--output_format=*)
|
||||
[ -n "$VIASH_PAR_OUTPUT_FORMAT" ] && ViashError Bad arguments for option \'--output_format=*\': \'$VIASH_PAR_OUTPUT_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_OUTPUT_FORMAT=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--pr_bases)
|
||||
[ -n "$VIASH_PAR_PR_BASES" ] && ViashError Bad arguments for option \'--pr_bases\': \'$VIASH_PAR_PR_BASES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_PR_BASES="$2"
|
||||
@@ -1987,26 +1960,37 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--qualimap_output_pdf)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_OUTPUT_PDF" ] && ViashError Bad arguments for option \'--qualimap_output_pdf\': \'$VIASH_PAR_QUALIMAP_OUTPUT_PDF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_OUTPUT_PDF="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --qualimap_output_pdf. Use "--help" to get more information on the parameters. && exit 1
|
||||
--qualimap_qc_report)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_QC_REPORT" ] && ViashError Bad arguments for option \'--qualimap_qc_report\': \'$VIASH_PAR_QUALIMAP_QC_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_QC_REPORT="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --qualimap_qc_report. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--qualimap_output_pdf=*)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_OUTPUT_PDF" ] && ViashError Bad arguments for option \'--qualimap_output_pdf=*\': \'$VIASH_PAR_QUALIMAP_OUTPUT_PDF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_OUTPUT_PDF=$(ViashRemoveFlags "$1")
|
||||
--qualimap_qc_report=*)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_QC_REPORT" ] && ViashError Bad arguments for option \'--qualimap_qc_report=*\': \'$VIASH_PAR_QUALIMAP_QC_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_QC_REPORT=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--qualimap_output_dir)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--qualimap_output_dir\': \'$VIASH_PAR_QUALIMAP_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_OUTPUT_DIR="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --qualimap_output_dir. Use "--help" to get more information on the parameters. && exit 1
|
||||
--qualimap_counts)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_COUNTS" ] && ViashError Bad arguments for option \'--qualimap_counts\': \'$VIASH_PAR_QUALIMAP_COUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_COUNTS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --qualimap_counts. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--qualimap_output_dir=*)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--qualimap_output_dir=*\': \'$VIASH_PAR_QUALIMAP_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_OUTPUT_DIR=$(ViashRemoveFlags "$1")
|
||||
--qualimap_counts=*)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_COUNTS" ] && ViashError Bad arguments for option \'--qualimap_counts=*\': \'$VIASH_PAR_QUALIMAP_COUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_COUNTS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--qualimap_report)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_REPORT" ] && ViashError Bad arguments for option \'--qualimap_report\': \'$VIASH_PAR_QUALIMAP_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_REPORT="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --qualimap_report. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--qualimap_report=*)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_REPORT" ] && ViashError Bad arguments for option \'--qualimap_report=*\': \'$VIASH_PAR_QUALIMAP_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_REPORT=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--deseq2_output)
|
||||
@@ -2488,9 +2472,6 @@ fi
|
||||
if [ -z ${VIASH_PAR_SUBTRACT_BACKGROUND+x} ]; then
|
||||
VIASH_PAR_SUBTRACT_BACKGROUND="false"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_OUTPUT_FORMAT+x} ]; then
|
||||
VIASH_PAR_OUTPUT_FORMAT="html"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_PR_BASES+x} ]; then
|
||||
VIASH_PAR_PR_BASES="100"
|
||||
fi
|
||||
@@ -2602,12 +2583,6 @@ fi
|
||||
if [ -z ${VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE+x} ]; then
|
||||
VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE="\$id.intercept_slope.txt"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_QUALIMAP_OUTPUT_PDF+x} ]; then
|
||||
VIASH_PAR_QUALIMAP_OUTPUT_PDF="\$id.qualimap_output.pdf"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_QUALIMAP_OUTPUT_DIR+x} ]; then
|
||||
VIASH_PAR_QUALIMAP_OUTPUT_DIR="\$id.qualimap_output"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_DESEQ2_OUTPUT+x} ]; then
|
||||
VIASH_PAR_DESEQ2_OUTPUT="deseq2"
|
||||
fi
|
||||
@@ -3093,18 +3068,6 @@ if [ ! -z "$VIASH_PAR_RSEQC_MODULES" ]; then
|
||||
unset IFS
|
||||
fi
|
||||
|
||||
if [ ! -z "$VIASH_PAR_OUTPUT_FORMAT" ]; then
|
||||
VIASH_PAR_OUTPUT_FORMAT_CHOICES=("html;pdf")
|
||||
IFS=';'
|
||||
set -f
|
||||
if ! [[ ";${VIASH_PAR_OUTPUT_FORMAT_CHOICES[*]};" =~ ";$VIASH_PAR_OUTPUT_FORMAT;" ]]; then
|
||||
ViashError '--output_format' specified value of \'$VIASH_PAR_OUTPUT_FORMAT\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
|
||||
exit 1
|
||||
fi
|
||||
set +f
|
||||
unset IFS
|
||||
fi
|
||||
|
||||
if [ ! -z "$VIASH_PAR_SEQUENCING_PROTOCOL" ]; then
|
||||
VIASH_PAR_SEQUENCING_PROTOCOL_CHOICES=("non-strand-specific;strand-specific-reverse;strand-specific-forward")
|
||||
IFS=';'
|
||||
@@ -3211,11 +3174,14 @@ fi
|
||||
if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE" ] && [ ! -d "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE")"
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_OUTPUT_PDF" ] && [ ! -d "$(dirname "$VIASH_PAR_QUALIMAP_OUTPUT_PDF")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_QUALIMAP_OUTPUT_PDF")"
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_QC_REPORT" ] && [ ! -d "$(dirname "$VIASH_PAR_QUALIMAP_QC_REPORT")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_QUALIMAP_QC_REPORT")"
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_QUALIMAP_OUTPUT_DIR")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_QUALIMAP_OUTPUT_DIR")"
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_COUNTS" ] && [ ! -d "$(dirname "$VIASH_PAR_QUALIMAP_COUNTS")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_QUALIMAP_COUNTS")"
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_REPORT" ] && [ ! -d "$(dirname "$VIASH_PAR_QUALIMAP_REPORT")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_QUALIMAP_REPORT")"
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_DESEQ2_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_DESEQ2_OUTPUT")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_DESEQ2_OUTPUT")"
|
||||
@@ -3298,22 +3264,22 @@ fi
|
||||
|
||||
|
||||
# set dependency paths
|
||||
VIASH_DEP_RSEQC_RSEQC_BAMSTAT="$VIASH_META_RESOURCES_DIR/../../../nextflow/rseqc/rseqc_bamstat/main.nf"
|
||||
VIASH_DEP_RSEQC_RSEQC_INFEREXPERIMENT="$VIASH_META_RESOURCES_DIR/../../../nextflow/rseqc/rseqc_inferexperiment/main.nf"
|
||||
VIASH_DEP_RSEQC_RSEQC_INNERDISTANCE="$VIASH_META_RESOURCES_DIR/../../../nextflow/rseqc/rseqc_innerdistance/main.nf"
|
||||
VIASH_DEP_RSEQC_RSEQC_JUNCTIONANNOTATION="$VIASH_META_RESOURCES_DIR/../../../nextflow/rseqc/rseqc_junctionannotation/main.nf"
|
||||
VIASH_DEP_RSEQC_RSEQC_JUNCTIONSATURATION="$VIASH_META_RESOURCES_DIR/../../../nextflow/rseqc/rseqc_junctionsaturation/main.nf"
|
||||
VIASH_DEP_RSEQC_RSEQC_READDISTRIBUTION="$VIASH_META_RESOURCES_DIR/../../../nextflow/rseqc/rseqc_readdistribution/main.nf"
|
||||
VIASH_DEP_RSEQC_RSEQC_READDUPLICATION="$VIASH_META_RESOURCES_DIR/../../../nextflow/rseqc/rseqc_readduplication/main.nf"
|
||||
VIASH_DEP_RSEQC_RSEQC_TIN="$VIASH_META_RESOURCES_DIR/../../../nextflow/rseqc/rseqc_tin/main.nf"
|
||||
VIASH_DEP_DUPRADAR="$VIASH_META_RESOURCES_DIR/../../../nextflow/dupradar/main.nf"
|
||||
VIASH_DEP_QUALIMAP="$VIASH_META_RESOURCES_DIR/../../../nextflow/qualimap/main.nf"
|
||||
VIASH_DEP_PRESEQ_LCEXTRAP="$VIASH_META_RESOURCES_DIR/../../../nextflow/preseq_lcextrap/main.nf"
|
||||
VIASH_DEP_MULTIQC_CUSTOM_BIOTYPE="$VIASH_META_RESOURCES_DIR/../../../nextflow/multiqc_custom_biotype/main.nf"
|
||||
VIASH_DEP_DESEQ2_QC="$VIASH_META_RESOURCES_DIR/../../../nextflow/deseq2_qc/main.nf"
|
||||
VIASH_DEP_PREPARE_MULTIQC_INPUT="$VIASH_META_RESOURCES_DIR/../../../nextflow/prepare_multiqc_input/main.nf"
|
||||
VIASH_DEP_RSEM_RSEM_MERGE_COUNTS="$VIASH_META_RESOURCES_DIR/../../../nextflow/rsem/rsem_merge_counts/main.nf"
|
||||
VIASH_DEP_RSEM_MERGE_COUNTS="$VIASH_META_RESOURCES_DIR/../../../nextflow/rsem_merge_counts/main.nf"
|
||||
VIASH_DEP_WORKFLOWS_MERGE_QUANT_RESULTS="$VIASH_META_RESOURCES_DIR/../../../nextflow/workflows/merge_quant_results/main.nf"
|
||||
VIASH_DEP_RSEQC_RSEQC_BAMSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_bamstat/main.nf"
|
||||
VIASH_DEP_RSEQC_RSEQC_INFEREXPERIMENT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inferexperiment/main.nf"
|
||||
VIASH_DEP_RSEQC_RSEQC_INNER_DISTANCE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inner_distance/main.nf"
|
||||
VIASH_DEP_QUALIMAP_QUALIMAP_RNASEQ="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/qualimap/qualimap_rnaseq/main.nf"
|
||||
VIASH_DEP_FEATURECOUNTS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf"
|
||||
VIASH_DEP_MULTIQC="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf"
|
||||
|
||||
@@ -3376,145 +3342,145 @@ workflow run_wf {
|
||||
]
|
||||
)
|
||||
|
||||
| multiqc_custom_biotype.run (
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.featurecounts && !state.skip_align },
|
||||
fromState: [
|
||||
"id": "id",
|
||||
"biocounts": "featurecounts",
|
||||
"biotypes_header": "biotypes_header"
|
||||
],
|
||||
toState: [
|
||||
"featurecounts_multiqc": "featurecounts_multiqc",
|
||||
"featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc"
|
||||
]
|
||||
)
|
||||
|
||||
| preseq_lcextrap.run (
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_preseq && !state.skip_align },
|
||||
fromState: [
|
||||
"paired": "paired",
|
||||
"input": "genome_bam",
|
||||
"extra_preseq_args": "extra_preseq_args"
|
||||
],
|
||||
toState: [ "preseq_output": "output" ]
|
||||
)
|
||||
|
||||
| rseqc_bamstat.run (
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "bam_stat" in state.rseqc_modules && !state.skip_align },
|
||||
fromState: [
|
||||
"input": "genome_bam",
|
||||
"map_qual": "map_qual"
|
||||
],
|
||||
toState: [ "bamstat_output": "output" ]
|
||||
)
|
||||
| rseqc_inferexperiment.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "infer_experiment" in state.rseqc_modules && !state.skip_align },
|
||||
fromState: [
|
||||
"input": "genome_bam",
|
||||
"refgene": "gene_bed",
|
||||
"sample_size": "sample_size",
|
||||
"map_qual": "map_qual"
|
||||
],
|
||||
toState: [ "strandedness_output": "output" ]
|
||||
)
|
||||
// Get predicted strandedness from the RSeQC infer_experiment.py output
|
||||
| map { id, state ->
|
||||
def inferred_strand = getInferexperimentStrandedness(state.strandedness_output, 30)
|
||||
def passed_strand_check = (state.strandedness != inferred_strand[0]) ? false : true
|
||||
[ id, state + [ inferred_strand: inferred_strand, passed_strand_check: passed_strand_check ] ]
|
||||
}
|
||||
| rseqc_innerdistance.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && state.paired && "inner_distance" in state.rseqc_modules && !state.skip_align },
|
||||
key: "inner_distance",
|
||||
fromState: [
|
||||
"input": "genome_bam",
|
||||
"refgene": "gene_bed",
|
||||
"sample_size": "sample_size",
|
||||
"map_qual": "map_qual",
|
||||
"lower_bound_size": "lower_bound_size",
|
||||
"upper_bound_size": "upper_bound_size",
|
||||
"step_size": "step_size"
|
||||
],
|
||||
toState: [
|
||||
"inner_dist_output_stats": "output_stats",
|
||||
"inner_dist_output_dist": "output_dist",
|
||||
"inner_dist_output_freq": "output_freq",
|
||||
"inner_dist_output_plot": "output_plot",
|
||||
"inner_dist_output_plot_r": "output_plot_r"
|
||||
]
|
||||
)
|
||||
| rseqc_junctionannotation.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_annotation" in state.rseqc_modules && !state.skip_align },
|
||||
fromState: [
|
||||
"input": "genome_bam",
|
||||
"refgene": "gene_bed",
|
||||
"map_qual": "map_qual",
|
||||
"min_intron": "min_intron"
|
||||
],
|
||||
toState: [
|
||||
"junction_annotation_output_log": "output_log",
|
||||
"junction_annotation_output_plot_r": "output_plot_r",
|
||||
"junction_annotation_output_junction_bed": "output_junction_bed",
|
||||
"junction_annotation_output_junction_interact": "output_junction_interact",
|
||||
"junction_annotation_output_junction_sheet": "output_junction_sheet",
|
||||
"junction_annotation_output_splice_events_plot": "output_splice_events_plot",
|
||||
"junction_annotation_output_splice_junctions_plot": "output_splice_junctions_plot"
|
||||
]
|
||||
)
|
||||
| rseqc_junctionsaturation.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_saturation" in state.rseqc_modules && !state.skip_align },
|
||||
fromState: [
|
||||
"input": "genome_bam",
|
||||
"refgene": "gene_bed",
|
||||
"sampling_percentile_lower_bound": "sampling_percentile_lower_bound",
|
||||
"sampling_percentile_upper_bound": "sampling_percentile_upper_bound",
|
||||
"sampling_percentile_step": "sampling_percentile_step",
|
||||
"min_intron": "min_intron",
|
||||
"min_splice_read": "min_splice_read",
|
||||
"map_qual": "map_qual"
|
||||
],
|
||||
toState: [
|
||||
"junction_saturation_output_plot_r": "output_plot_r",
|
||||
"junction_saturation_output_plot": "output_plot"
|
||||
]
|
||||
)
|
||||
| rseqc_readdistribution.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_distribution" in state.rseqc_modules && !state.skip_align },
|
||||
fromState: [
|
||||
"input": "genome_bam",
|
||||
"refgene": "gene_bed",
|
||||
],
|
||||
toState: [ "read_distribution_output": "output" ]
|
||||
)
|
||||
| rseqc_readduplication.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_duplication" in state.rseqc_modules && !state.skip_align },
|
||||
fromState: [
|
||||
"input": "genome_bam",
|
||||
"read_count_upper_limit": "read_count_upper_limit",
|
||||
"map_qual": "map_qual"
|
||||
],
|
||||
toState: [
|
||||
"read_duplication_output_duplication_rate_plot_r": "output_duplication_rate_plot_r",
|
||||
"read_duplication_output_duplication_rate_plot": "output_duplication_rate_plot",
|
||||
"read_duplication_output_duplication_rate_mapping": "output_duplication_rate_mapping",
|
||||
"read_duplication_output_duplication_rate_sequence": "output_duplication_rate_sequence"
|
||||
]
|
||||
)
|
||||
| rseqc_tin.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "tin" in state.rseqc_modules && !state.skip_align },
|
||||
fromState: [
|
||||
"bam_input": "genome_bam",
|
||||
"bai_input": "genome_bam_index",
|
||||
"refgene": "gene_bed",
|
||||
"minimum_coverage": "minimum_coverage",
|
||||
"sample_size": "tin_sample_size",
|
||||
"subtract_background": "subtract_background"
|
||||
],
|
||||
toState: [
|
||||
"tin_output_summary": "output_tin_summary",
|
||||
"tin_output_metrics": "output_tin"
|
||||
]
|
||||
)
|
||||
| multiqc_custom_biotype.run (
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.featurecounts && !state.skip_align },
|
||||
fromState: [
|
||||
"id": "id",
|
||||
"biocounts": "featurecounts",
|
||||
"biotypes_header": "biotypes_header"
|
||||
],
|
||||
toState: [
|
||||
"featurecounts_multiqc": "featurecounts_multiqc",
|
||||
"featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc"
|
||||
]
|
||||
)
|
||||
|
||||
| preseq_lcextrap.run (
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_preseq && !state.skip_align },
|
||||
fromState: [
|
||||
"paired": "paired",
|
||||
"input": "genome_bam",
|
||||
"extra_preseq_args": "extra_preseq_args"
|
||||
],
|
||||
toState: [ "preseq_output": "output" ]
|
||||
)
|
||||
|
||||
| rseqc_bamstat.run (
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "bam_stat" in state.rseqc_modules && !state.skip_align },
|
||||
fromState: [
|
||||
"input_file": "genome_bam",
|
||||
"mapq": "map_qual"
|
||||
],
|
||||
toState: [ "bamstat_output": "output" ]
|
||||
)
|
||||
| rseqc_inferexperiment.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "infer_experiment" in state.rseqc_modules && !state.skip_align },
|
||||
fromState: [
|
||||
"input_file": "genome_bam",
|
||||
"refgene": "gene_bed",
|
||||
"sample_size": "sample_size",
|
||||
"mapq": "map_qual"
|
||||
],
|
||||
toState: [ "strandedness_output": "output" ]
|
||||
)
|
||||
// Get predicted strandedness from the RSeQC infer_experiment.py output
|
||||
| map { id, state ->
|
||||
def inferred_strand = getInferexperimentStrandedness(state.strandedness_output, 30)
|
||||
def passed_strand_check = (state.strandedness != inferred_strand[0]) ? false : true
|
||||
[ id, state + [ inferred_strand: inferred_strand, passed_strand_check: passed_strand_check ] ]
|
||||
}
|
||||
| rseqc_inner_distance.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && state.paired && "inner_distance" in state.rseqc_modules && !state.skip_align },
|
||||
key: "inner_distance",
|
||||
fromState: [
|
||||
"input_file": "genome_bam",
|
||||
"refgene": "gene_bed",
|
||||
"sample_size": "sample_size",
|
||||
"mapq": "map_qual",
|
||||
"lower_bound": "lower_bound_size",
|
||||
"upper_bound": "upper_bound_size",
|
||||
"step": "step_size"
|
||||
],
|
||||
toState: [
|
||||
"inner_dist_output_stats": "output_stats",
|
||||
"inner_dist_output_dist": "output_dist",
|
||||
"inner_dist_output_freq": "output_freq",
|
||||
"inner_dist_output_plot": "output_plot",
|
||||
"inner_dist_output_plot_r": "output_plot_r"
|
||||
]
|
||||
)
|
||||
| rseqc_junctionannotation.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_annotation" in state.rseqc_modules && !state.skip_align },
|
||||
fromState: [
|
||||
"input": "genome_bam",
|
||||
"refgene": "gene_bed",
|
||||
"map_qual": "map_qual",
|
||||
"min_intron": "min_intron"
|
||||
],
|
||||
toState: [
|
||||
"junction_annotation_output_log": "output_log",
|
||||
"junction_annotation_output_plot_r": "output_plot_r",
|
||||
"junction_annotation_output_junction_bed": "output_junction_bed",
|
||||
"junction_annotation_output_junction_interact": "output_junction_interact",
|
||||
"junction_annotation_output_junction_sheet": "output_junction_sheet",
|
||||
"junction_annotation_output_splice_events_plot": "output_splice_events_plot",
|
||||
"junction_annotation_output_splice_junctions_plot": "output_splice_junctions_plot"
|
||||
]
|
||||
)
|
||||
| rseqc_junctionsaturation.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_saturation" in state.rseqc_modules && !state.skip_align },
|
||||
fromState: [
|
||||
"input": "genome_bam",
|
||||
"refgene": "gene_bed",
|
||||
"sampling_percentile_lower_bound": "sampling_percentile_lower_bound",
|
||||
"sampling_percentile_upper_bound": "sampling_percentile_upper_bound",
|
||||
"sampling_percentile_step": "sampling_percentile_step",
|
||||
"min_intron": "min_intron",
|
||||
"min_splice_read": "min_splice_read",
|
||||
"map_qual": "map_qual"
|
||||
],
|
||||
toState: [
|
||||
"junction_saturation_output_plot_r": "output_plot_r",
|
||||
"junction_saturation_output_plot": "output_plot"
|
||||
]
|
||||
)
|
||||
| rseqc_readdistribution.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_distribution" in state.rseqc_modules && !state.skip_align },
|
||||
fromState: [
|
||||
"input": "genome_bam",
|
||||
"refgene": "gene_bed",
|
||||
],
|
||||
toState: [ "read_distribution_output": "output" ]
|
||||
)
|
||||
| rseqc_readduplication.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_duplication" in state.rseqc_modules && !state.skip_align },
|
||||
fromState: [
|
||||
"input": "genome_bam",
|
||||
"read_count_upper_limit": "read_count_upper_limit",
|
||||
"map_qual": "map_qual"
|
||||
],
|
||||
toState: [
|
||||
"read_duplication_output_duplication_rate_plot_r": "output_duplication_rate_plot_r",
|
||||
"read_duplication_output_duplication_rate_plot": "output_duplication_rate_plot",
|
||||
"read_duplication_output_duplication_rate_mapping": "output_duplication_rate_mapping",
|
||||
"read_duplication_output_duplication_rate_sequence": "output_duplication_rate_sequence"
|
||||
]
|
||||
)
|
||||
| rseqc_tin.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "tin" in state.rseqc_modules && !state.skip_align },
|
||||
fromState: [
|
||||
"bam_input": "genome_bam",
|
||||
"bai_input": "genome_bam_index",
|
||||
"refgene": "gene_bed",
|
||||
"minimum_coverage": "minimum_coverage",
|
||||
"sample_size": "tin_sample_size",
|
||||
"subtract_background": "subtract_background"
|
||||
],
|
||||
toState: [
|
||||
"tin_output_summary": "output_tin_summary",
|
||||
"tin_output_metrics": "output_tin"
|
||||
]
|
||||
)
|
||||
|
||||
| dupradar.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_dupradar && !state.skip_align },
|
||||
@@ -3536,23 +3502,25 @@ workflow run_wf {
|
||||
]
|
||||
)
|
||||
|
||||
| qualimap.run(
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_qualimap && !state.skip_align },
|
||||
fromState: [
|
||||
"input": "genome_bam",
|
||||
"gtf": "gtf",
|
||||
"pr_bases": "pr_bases",
|
||||
"tr_bias": "tr_bias",
|
||||
"algorithm": "algorithm",
|
||||
"sequencing_protocol": "sequencing_protocol",
|
||||
"sorted": "sorted",
|
||||
"java_memory_size": "java_memory_size",
|
||||
],
|
||||
toState: [
|
||||
"qualimap_output_pdf": "output_pdf",
|
||||
"qualimap_output_dir": "output_dir"
|
||||
]
|
||||
)
|
||||
// TODO: Add outdir as an output argument to the qualimap module on biobox.
|
||||
// Qualimap ouputs a few more raw data files to outdir but since the module is using a temporary directory as output dir these files are lost.
|
||||
| qualimap_rnaseq.run(
|
||||
fromState: [
|
||||
"bam": "genome_bam",
|
||||
"gtf": "gtf",
|
||||
"num_pr_bases": "pr_bases",
|
||||
"num_tr_bias": "tr_bias",
|
||||
"algorithm": "algorithm",
|
||||
"sequencing_protocol": "sequencing_protocol",
|
||||
"sorted": "sorted",
|
||||
"java_memory_size": "java_memory_size",
|
||||
],
|
||||
toState: [
|
||||
"qualimap_report": "report",
|
||||
"qualimap_qc_report": "qc_report",
|
||||
"qualimap_counts": "counts"
|
||||
]
|
||||
)
|
||||
|
||||
merged_ch = qc_ch
|
||||
| toSortedList
|
||||
@@ -3675,10 +3643,10 @@ workflow run_wf {
|
||||
(state.preseq_output instanceof java.nio.file.Path && state.preseq_output.exists()) ?
|
||||
state.preseq_output :
|
||||
null }
|
||||
def qualimap_output_dir = list.collect { id, state ->
|
||||
(state.qualimap_output_dir instanceof java.nio.file.Path && state.qualimap_output_dir.exists()) ?
|
||||
state.qualimap_output_dir :
|
||||
null }
|
||||
// def qualimap_output_dir = list.collect { id, state ->
|
||||
// (state.qualimap_output_dir instanceof java.nio.file.Path && state.qualimap_output_dir.exists()) ?
|
||||
// state.qualimap_output_dir :
|
||||
// null }
|
||||
def dupradar_output_dup_intercept_mqc = list.collect { id, state ->
|
||||
(state.dupradar_output_dup_intercept_mqc instanceof java.nio.file.Path && state.dupradar_output_dup_intercept_mqc.exists()) ?
|
||||
state.dupradar_output_dup_intercept_mqc :
|
||||
@@ -3763,7 +3731,7 @@ workflow run_wf {
|
||||
featurecounts_multiqc: featurecounts_multiqc,
|
||||
featurecounts_rrna_multiqc: featurecounts_rrna_multiqc,
|
||||
preseq_output: preseq_output,
|
||||
qualimap_output_dir: qualimap_output_dir,
|
||||
// qualimap_output_dir: qualimap_output_dir,
|
||||
dupradar_output_dup_intercept_mqc: dupradar_output_dup_intercept_mqc,
|
||||
dupradar_output_duprate_exp_denscurve_mqc: dupradar_output_duprate_exp_denscurve_mqc,
|
||||
bamstat_output: bamstat_output,
|
||||
@@ -3942,7 +3910,7 @@ workflow run_wf {
|
||||
"pseudo_aligner_pca_multiqc": "deseq2_pca_multiqc_pseudo",
|
||||
"pseudo_aligner_clustering_multiqc": "deseq2_dists_multiqc_pseudo",
|
||||
"preseq_multiqc": "preseq_output",
|
||||
"qualimap_multiqc": "qualimap_output_dir",
|
||||
// "qualimap_multiqc": "qualimap_output_dir",
|
||||
"dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc",
|
||||
"dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc",
|
||||
"bamstat_multiqc": "bamstat_output",
|
||||
@@ -4042,8 +4010,9 @@ workflow run_wf {
|
||||
"dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc",
|
||||
"dupradar_output_expression_histogram": "dupradar_output_expression_histogram",
|
||||
"dupradar_output_intercept_slope": "dupradar_output_intercept_slope",
|
||||
"qualimap_output_dir": "qualimap_output_dir",
|
||||
"qualimap_output_pdf": "qualimap_output_pdf",
|
||||
"qualimap_report": "qualimap_report",
|
||||
"qualimap_qc_report": "qualimap_qc_report",
|
||||
"qualimap_counts": "qualimap_counts",
|
||||
"featurecounts": "featurecounts",
|
||||
"featurecounts_summary": "featurecounts_summary",
|
||||
"featurecounts_multiqc": "featurecounts_multiqc",
|
||||
@@ -4241,8 +4210,16 @@ if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE" ] && [ ! -e "$VIASH_PAR_D
|
||||
ViashError "Output file '$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ] && [ ! -e "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ]; then
|
||||
ViashError "Output file '$VIASH_PAR_QUALIMAP_OUTPUT_DIR' does not exist."
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_QC_REPORT" ] && [ ! -e "$VIASH_PAR_QUALIMAP_QC_REPORT" ]; then
|
||||
ViashError "Output file '$VIASH_PAR_QUALIMAP_QC_REPORT' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_COUNTS" ] && [ ! -e "$VIASH_PAR_QUALIMAP_COUNTS" ]; then
|
||||
ViashError "Output file '$VIASH_PAR_QUALIMAP_COUNTS' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_REPORT" ] && [ ! -e "$VIASH_PAR_QUALIMAP_REPORT" ]; then
|
||||
ViashError "Output file '$VIASH_PAR_QUALIMAP_REPORT' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_DESEQ2_OUTPUT" ] && [ ! -e "$VIASH_PAR_DESEQ2_OUTPUT" ]; then
|
||||
|
||||
@@ -237,24 +237,6 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_trimgalore_args"
|
||||
description: "Extra arguments to pass to Trim Galore! command in addition to defaults\
|
||||
\ defined by the pipeline."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_fastp_args"
|
||||
description: "Extra arguments to pass to fastp command in addition to defaults\
|
||||
\ defined by the pipeline."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--min_trimmed_reads"
|
||||
description: "Minimum number of trimmed reads below which samples are removed\
|
||||
@@ -271,16 +253,14 @@ argument_groups:
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--bbsplit_fasta_list"
|
||||
description: "Path to comma-separated file containing a list of reference genomes\
|
||||
\ to filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must\
|
||||
\ be explicitly set to \"false\". The file should contain 2 (comma separated)\
|
||||
\ columns - short name and full path to reference genome(s)"
|
||||
description: "List of reference genomes (separated by \";\") to filter reads against\
|
||||
\ with BBSplit."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--bbsplit_index"
|
||||
@@ -437,7 +417,7 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
- type: "double"
|
||||
name: "--kallisto_quant_fragment_length"
|
||||
description: "For single-end mode only, the estimated average fragment length\
|
||||
\ to use for quantification with Kallisto."
|
||||
@@ -446,7 +426,7 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
- type: "double"
|
||||
name: "--kallisto_quant_fragment_length_sd"
|
||||
description: "For single-end mode only, the estimated standard deviation of the\
|
||||
\ fragment length for quantification with Kallisto."
|
||||
@@ -470,17 +450,6 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_salmon_quant_args"
|
||||
description: "Extra arguments to pass to salmon quant command in addition to defaults\
|
||||
\ defined by the pipeline."
|
||||
info: null
|
||||
default:
|
||||
- "-v"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--min_mapped_reads"
|
||||
description: "Minimum percentage of uniquely mapped reads below which samples\
|
||||
@@ -530,18 +499,6 @@ argument_groups:
|
||||
description: "Skip all of the pseudo-alignment-based processes within the pipeline."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "string"
|
||||
name: "--extra_rsem_calculate_expression_args"
|
||||
description: "Extra arguments to pass to rsem-calculate-expression command in\
|
||||
\ addition to defaults defined by the pipeline."
|
||||
info: null
|
||||
default:
|
||||
- "--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed\
|
||||
\ 1"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Process skipping options"
|
||||
arguments:
|
||||
- type: "boolean"
|
||||
@@ -636,17 +593,6 @@ argument_groups:
|
||||
direction: "input"
|
||||
- name: "Other process arguments"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--extra_fq_subsample_args"
|
||||
description: "Extra arguments to pass to fq subsample command in addition to defaults\
|
||||
\ defined by the pipeline."
|
||||
info: null
|
||||
default:
|
||||
- " --record-count 1000000 --seed 1"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_picard_args"
|
||||
description: "Extra arguments to pass to picard MarkDuplicates command in addition\
|
||||
@@ -659,17 +605,6 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_bedtools_args"
|
||||
description: "Extra arguments to pass to bedtools genomecov command in addition\
|
||||
\ to defaults defined by the pipeline."
|
||||
info: null
|
||||
default:
|
||||
- " -split -du"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_preseq_args"
|
||||
description: "Extra arguments to pass to preseq lc_extrap command in addition\
|
||||
@@ -840,7 +775,7 @@ argument_groups:
|
||||
description: "Path to output directory"
|
||||
info: null
|
||||
default:
|
||||
- "fastq/$id.read_1.fastq.gz"
|
||||
- "fastq/${id}_r1.fastq.gz"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -852,7 +787,7 @@ argument_groups:
|
||||
description: "Path to output directory"
|
||||
info: null
|
||||
default:
|
||||
- "fastq/$id.read_2.fastq.gz"
|
||||
- "fastq/${id}_r2.fastq.gz"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -864,7 +799,7 @@ argument_groups:
|
||||
description: "FastQC HTML report for read 1."
|
||||
info: null
|
||||
default:
|
||||
- "fastqc_raw/$id.read_1.fastqc.html"
|
||||
- "fastqc_raw/${id}_r1.fastqc.html"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -876,7 +811,7 @@ argument_groups:
|
||||
description: "FastQC HTML report for read 2."
|
||||
info: null
|
||||
default:
|
||||
- "fastqc_raw/$id.read_2.fastqc.html"
|
||||
- "fastqc_raw/${id}_r2.fastqc.html"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -888,7 +823,7 @@ argument_groups:
|
||||
description: "FastQC report archive for read 1."
|
||||
info: null
|
||||
default:
|
||||
- "fastqc_raw/$id.read_1.fastqc.zip"
|
||||
- "fastqc_raw/${id}_r1.fastqc.zip"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -900,7 +835,7 @@ argument_groups:
|
||||
description: "FastQC report archive for read 2."
|
||||
info: null
|
||||
default:
|
||||
- "fastqc_raw/$id.read_2.fastqc.zip"
|
||||
- "fastqc_raw/${id}_r2.fastqc.zip"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -911,7 +846,7 @@ argument_groups:
|
||||
name: "--trim_html_1"
|
||||
info: null
|
||||
default:
|
||||
- "fastqc_trim/$id.read_1.trimmed_fastqc.html"
|
||||
- "fastqc_trim/${id}_r1.trimmed_fastqc.html"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -922,7 +857,7 @@ argument_groups:
|
||||
name: "--trim_html_2"
|
||||
info: null
|
||||
default:
|
||||
- "fastqc_trim/$id.read_2.trimmed_fastqc.html"
|
||||
- "fastqc_trim/${id}_r2.trimmed_fastqc.html"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -933,7 +868,7 @@ argument_groups:
|
||||
name: "--trim_zip_1"
|
||||
info: null
|
||||
default:
|
||||
- "fastqc_trim/$id.read_1.trimmed_fastqc.zip"
|
||||
- "fastqc_trim/${id}_r1.trimmed_fastqc.zip"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -944,7 +879,7 @@ argument_groups:
|
||||
name: "--trim_zip_2"
|
||||
info: null
|
||||
default:
|
||||
- "fastqc_trim/$id.read_2.trimmed_fastqc.zip"
|
||||
- "fastqc_trim/${id}_r2.trimmed_fastqc.zip"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -955,7 +890,7 @@ argument_groups:
|
||||
name: "--trim_log_1"
|
||||
info: null
|
||||
default:
|
||||
- "trimgalore/$id.read_1.trimming_report.txt"
|
||||
- "trimgalore/${id}_r1.trimming_report.txt"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -966,7 +901,7 @@ argument_groups:
|
||||
name: "--trim_log_2"
|
||||
info: null
|
||||
default:
|
||||
- "trimgalore/$id.read_2.trimming_report.txt"
|
||||
- "trimgalore/${id}_r2.trimming_report.txt"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -1833,21 +1768,35 @@ argument_groups:
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--qualimap_output_pdf"
|
||||
name: "--qualimap_qc_report"
|
||||
description: "Text file containing the RNAseq QC results."
|
||||
info: null
|
||||
default:
|
||||
- "qualimap/$id.qualimap_output.pdf"
|
||||
must_exist: false
|
||||
- "Qualimap/$id.rnaseq_qc_results.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--qualimap_output_dir"
|
||||
name: "--qualimap_counts"
|
||||
description: "Output file for computed counts."
|
||||
info: null
|
||||
default:
|
||||
- "qualimap/$id"
|
||||
- "Qualimap/$id.counts.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--qualimap_report"
|
||||
description: "Report output file. Supported formats are PDF or HTML."
|
||||
info: null
|
||||
default:
|
||||
- "Qualimap/$id.report.html"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -2031,7 +1980,7 @@ dependencies:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
@@ -2112,8 +2061,8 @@ build_info:
|
||||
output: "target/executable/workflows/rnaseq"
|
||||
executable: "target/executable/workflows/rnaseq/rnaseq"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
|
||||
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
|
||||
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
|
||||
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/nextflow/workflows/prepare_genome"
|
||||
- "target/nextflow/cat_fastq"
|
||||
@@ -2132,7 +2081,7 @@ package_config:
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
repo: "biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
|
||||
@@ -283,16 +283,6 @@ function ViashHelp {
|
||||
echo " choices: [ trimgalore, fastp ]"
|
||||
echo " Specify the trimming tool to use."
|
||||
echo ""
|
||||
echo " --extra_trimgalore_args"
|
||||
echo " type: string"
|
||||
echo " Extra arguments to pass to Trim Galore! command in addition to defaults"
|
||||
echo " defined by the pipeline."
|
||||
echo ""
|
||||
echo " --extra_fastp_args"
|
||||
echo " type: string"
|
||||
echo " Extra arguments to pass to fastp command in addition to defaults defined"
|
||||
echo " by the pipeline."
|
||||
echo ""
|
||||
echo " --min_trimmed_reads"
|
||||
echo " type: integer"
|
||||
echo " default: 10000"
|
||||
@@ -302,11 +292,9 @@ function ViashHelp {
|
||||
echo ""
|
||||
echo "Read filtering options:"
|
||||
echo " --bbsplit_fasta_list"
|
||||
echo " type: file, file must exist"
|
||||
echo " Path to comma-separated file containing a list of reference genomes to"
|
||||
echo " filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must"
|
||||
echo " be explicitly set to \"false\". The file should contain 2 (comma"
|
||||
echo " separated) columns - short name and full path to reference genome(s)"
|
||||
echo " type: file, multiple values allowed, file must exist"
|
||||
echo " List of reference genomes (separated by \";\") to filter reads against"
|
||||
echo " with BBSplit."
|
||||
echo ""
|
||||
echo " --bbsplit_index"
|
||||
echo " type: file, file must exist"
|
||||
@@ -389,12 +377,12 @@ function ViashHelp {
|
||||
echo " Kmer length passed to indexing step of pseudoaligners."
|
||||
echo ""
|
||||
echo " --kallisto_quant_fragment_length"
|
||||
echo " type: integer"
|
||||
echo " type: double"
|
||||
echo " For single-end mode only, the estimated average fragment length to use"
|
||||
echo " for quantification with Kallisto."
|
||||
echo ""
|
||||
echo " --kallisto_quant_fragment_length_sd"
|
||||
echo " type: integer"
|
||||
echo " type: double"
|
||||
echo " For single-end mode only, the estimated standard deviation of the"
|
||||
echo " fragment length for quantification with Kallisto."
|
||||
echo ""
|
||||
@@ -408,12 +396,6 @@ function ViashHelp {
|
||||
echo " Override Salmon library type inferred based on strandedness defined in"
|
||||
echo " meta object."
|
||||
echo ""
|
||||
echo " --extra_salmon_quant_args"
|
||||
echo " type: string"
|
||||
echo " default: -v"
|
||||
echo " Extra arguments to pass to salmon quant command in addition to defaults"
|
||||
echo " defined by the pipeline."
|
||||
echo ""
|
||||
echo " --min_mapped_reads"
|
||||
echo " type: integer"
|
||||
echo " default: 5"
|
||||
@@ -448,13 +430,6 @@ function ViashHelp {
|
||||
echo " type: boolean_true"
|
||||
echo " Skip all of the pseudo-alignment-based processes within the pipeline."
|
||||
echo ""
|
||||
echo " --extra_rsem_calculate_expression_args"
|
||||
echo " type: string"
|
||||
echo " default: --star --star-output-genome-bam --star-gzipped-read-file"
|
||||
echo "--estimate-rspd --seed 1"
|
||||
echo " Extra arguments to pass to rsem-calculate-expression command in addition"
|
||||
echo " to defaults defined by the pipeline."
|
||||
echo ""
|
||||
echo "Process skipping options:"
|
||||
echo " --skip_fastqc"
|
||||
echo " type: boolean"
|
||||
@@ -520,12 +495,6 @@ function ViashHelp {
|
||||
echo " Skip MultiQC."
|
||||
echo ""
|
||||
echo "Other process arguments:"
|
||||
echo " --extra_fq_subsample_args"
|
||||
echo " type: string"
|
||||
echo " default: --record-count 1000000 --seed 1"
|
||||
echo " Extra arguments to pass to fq subsample command in addition to defaults"
|
||||
echo " defined by the pipeline."
|
||||
echo ""
|
||||
echo " --extra_picard_args"
|
||||
echo " type: string"
|
||||
echo " default: --ASSUME_SORTED true --REMOVE_DUPLICATES false"
|
||||
@@ -533,12 +502,6 @@ function ViashHelp {
|
||||
echo " Extra arguments to pass to picard MarkDuplicates command in addition to"
|
||||
echo " defaults defined by the pipeline."
|
||||
echo ""
|
||||
echo " --extra_bedtools_args"
|
||||
echo " type: string"
|
||||
echo " default: -split -du"
|
||||
echo " Extra arguments to pass to bedtools genomecov command in addition to"
|
||||
echo " defaults defined by the pipeline."
|
||||
echo ""
|
||||
echo " --extra_preseq_args"
|
||||
echo " type: string"
|
||||
echo " default: -verbose -seed 1 -seg_len 100000000"
|
||||
@@ -610,57 +573,57 @@ function ViashHelp {
|
||||
echo ""
|
||||
echo " --output_fastq_1"
|
||||
echo " type: file, output"
|
||||
echo " default: fastq/\$id.read_1.fastq.gz"
|
||||
echo " default: fastq/\${id}_r1.fastq.gz"
|
||||
echo " Path to output directory"
|
||||
echo ""
|
||||
echo " --output_fastq_2"
|
||||
echo " type: file, output"
|
||||
echo " default: fastq/\$id.read_2.fastq.gz"
|
||||
echo " default: fastq/\${id}_r2.fastq.gz"
|
||||
echo " Path to output directory"
|
||||
echo ""
|
||||
echo " --fastqc_html_1"
|
||||
echo " type: file, output"
|
||||
echo " default: fastqc_raw/\$id.read_1.fastqc.html"
|
||||
echo " default: fastqc_raw/\${id}_r1.fastqc.html"
|
||||
echo " FastQC HTML report for read 1."
|
||||
echo ""
|
||||
echo " --fastqc_html_2"
|
||||
echo " type: file, output"
|
||||
echo " default: fastqc_raw/\$id.read_2.fastqc.html"
|
||||
echo " default: fastqc_raw/\${id}_r2.fastqc.html"
|
||||
echo " FastQC HTML report for read 2."
|
||||
echo ""
|
||||
echo " --fastqc_zip_1"
|
||||
echo " type: file, output"
|
||||
echo " default: fastqc_raw/\$id.read_1.fastqc.zip"
|
||||
echo " default: fastqc_raw/\${id}_r1.fastqc.zip"
|
||||
echo " FastQC report archive for read 1."
|
||||
echo ""
|
||||
echo " --fastqc_zip_2"
|
||||
echo " type: file, output"
|
||||
echo " default: fastqc_raw/\$id.read_2.fastqc.zip"
|
||||
echo " default: fastqc_raw/\${id}_r2.fastqc.zip"
|
||||
echo " FastQC report archive for read 2."
|
||||
echo ""
|
||||
echo " --trim_html_1"
|
||||
echo " type: file, output"
|
||||
echo " default: fastqc_trim/\$id.read_1.trimmed_fastqc.html"
|
||||
echo " default: fastqc_trim/\${id}_r1.trimmed_fastqc.html"
|
||||
echo ""
|
||||
echo " --trim_html_2"
|
||||
echo " type: file, output"
|
||||
echo " default: fastqc_trim/\$id.read_2.trimmed_fastqc.html"
|
||||
echo " default: fastqc_trim/\${id}_r2.trimmed_fastqc.html"
|
||||
echo ""
|
||||
echo " --trim_zip_1"
|
||||
echo " type: file, output"
|
||||
echo " default: fastqc_trim/\$id.read_1.trimmed_fastqc.zip"
|
||||
echo " default: fastqc_trim/\${id}_r1.trimmed_fastqc.zip"
|
||||
echo ""
|
||||
echo " --trim_zip_2"
|
||||
echo " type: file, output"
|
||||
echo " default: fastqc_trim/\$id.read_2.trimmed_fastqc.zip"
|
||||
echo " default: fastqc_trim/\${id}_r2.trimmed_fastqc.zip"
|
||||
echo ""
|
||||
echo " --trim_log_1"
|
||||
echo " type: file, output"
|
||||
echo " default: trimgalore/\$id.read_1.trimming_report.txt"
|
||||
echo " default: trimgalore/\${id}_r1.trimming_report.txt"
|
||||
echo ""
|
||||
echo " --trim_log_2"
|
||||
echo " type: file, output"
|
||||
echo " default: trimgalore/\$id.read_2.trimming_report.txt"
|
||||
echo " default: trimgalore/\${id}_r2.trimming_report.txt"
|
||||
echo ""
|
||||
echo " --fastp_trim_json"
|
||||
echo " type: file, output, file must exist"
|
||||
@@ -1004,13 +967,20 @@ function ViashHelp {
|
||||
echo " type: file, output, file must exist"
|
||||
echo " default: dupradar/intercept_slope/\$id.intercept_slope.txt"
|
||||
echo ""
|
||||
echo " --qualimap_output_pdf"
|
||||
echo " type: file, output"
|
||||
echo " default: qualimap/\$id.qualimap_output.pdf"
|
||||
echo ""
|
||||
echo " --qualimap_output_dir"
|
||||
echo " --qualimap_qc_report"
|
||||
echo " type: file, output, file must exist"
|
||||
echo " default: qualimap/\$id"
|
||||
echo " default: Qualimap/\$id.rnaseq_qc_results.txt"
|
||||
echo " Text file containing the RNAseq QC results."
|
||||
echo ""
|
||||
echo " --qualimap_counts"
|
||||
echo " type: file, output, file must exist"
|
||||
echo " default: Qualimap/\$id.counts.txt"
|
||||
echo " Output file for computed counts."
|
||||
echo ""
|
||||
echo " --qualimap_report"
|
||||
echo " type: file, output, file must exist"
|
||||
echo " default: Qualimap/\$id.report.html"
|
||||
echo " Report output file. Supported formats are PDF or HTML."
|
||||
echo ""
|
||||
echo " --deseq2_output"
|
||||
echo " type: file, output, file must exist"
|
||||
@@ -1342,28 +1312,6 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_TRIMMER=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--extra_trimgalore_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_TRIMGALORE_ARGS" ] && ViashError Bad arguments for option \'--extra_trimgalore_args\': \'$VIASH_PAR_EXTRA_TRIMGALORE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_TRIMGALORE_ARGS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_trimgalore_args. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_trimgalore_args=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_TRIMGALORE_ARGS" ] && ViashError Bad arguments for option \'--extra_trimgalore_args=*\': \'$VIASH_PAR_EXTRA_TRIMGALORE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_TRIMGALORE_ARGS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--extra_fastp_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_FASTP_ARGS" ] && ViashError Bad arguments for option \'--extra_fastp_args\': \'$VIASH_PAR_EXTRA_FASTP_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_FASTP_ARGS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_fastp_args. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_fastp_args=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_FASTP_ARGS" ] && ViashError Bad arguments for option \'--extra_fastp_args=*\': \'$VIASH_PAR_EXTRA_FASTP_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_FASTP_ARGS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--min_trimmed_reads)
|
||||
[ -n "$VIASH_PAR_MIN_TRIMMED_READS" ] && ViashError Bad arguments for option \'--min_trimmed_reads\': \'$VIASH_PAR_MIN_TRIMMED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_MIN_TRIMMED_READS="$2"
|
||||
@@ -1376,14 +1324,20 @@ while [[ $# -gt 0 ]]; do
|
||||
shift 1
|
||||
;;
|
||||
--bbsplit_fasta_list)
|
||||
[ -n "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && ViashError Bad arguments for option \'--bbsplit_fasta_list\': \'$VIASH_PAR_BBSPLIT_FASTA_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_BBSPLIT_FASTA_LIST="$2"
|
||||
if [ -z "$VIASH_PAR_BBSPLIT_FASTA_LIST" ]; then
|
||||
VIASH_PAR_BBSPLIT_FASTA_LIST="$2"
|
||||
else
|
||||
VIASH_PAR_BBSPLIT_FASTA_LIST="$VIASH_PAR_BBSPLIT_FASTA_LIST;""$2"
|
||||
fi
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bbsplit_fasta_list. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--bbsplit_fasta_list=*)
|
||||
[ -n "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && ViashError Bad arguments for option \'--bbsplit_fasta_list=*\': \'$VIASH_PAR_BBSPLIT_FASTA_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_BBSPLIT_FASTA_LIST=$(ViashRemoveFlags "$1")
|
||||
if [ -z "$VIASH_PAR_BBSPLIT_FASTA_LIST" ]; then
|
||||
VIASH_PAR_BBSPLIT_FASTA_LIST=$(ViashRemoveFlags "$1")
|
||||
else
|
||||
VIASH_PAR_BBSPLIT_FASTA_LIST="$VIASH_PAR_BBSPLIT_FASTA_LIST;"$(ViashRemoveFlags "$1")
|
||||
fi
|
||||
shift 1
|
||||
;;
|
||||
--bbsplit_index)
|
||||
@@ -1560,17 +1514,6 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_SALMON_QUANT_LIBTYPE=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--extra_salmon_quant_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS" ] && ViashError Bad arguments for option \'--extra_salmon_quant_args\': \'$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_SALMON_QUANT_ARGS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_salmon_quant_args. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_salmon_quant_args=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS" ] && ViashError Bad arguments for option \'--extra_salmon_quant_args=*\': \'$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_SALMON_QUANT_ARGS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--min_mapped_reads)
|
||||
[ -n "$VIASH_PAR_MIN_MAPPED_READS" ] && ViashError Bad arguments for option \'--min_mapped_reads\': \'$VIASH_PAR_MIN_MAPPED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_MIN_MAPPED_READS="$2"
|
||||
@@ -1618,17 +1561,6 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_SKIP_PSEUDO_ALIGNMENT=true
|
||||
shift 1
|
||||
;;
|
||||
--extra_rsem_calculate_expression_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS" ] && ViashError Bad arguments for option \'--extra_rsem_calculate_expression_args\': \'$VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_rsem_calculate_expression_args. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_rsem_calculate_expression_args=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS" ] && ViashError Bad arguments for option \'--extra_rsem_calculate_expression_args=*\': \'$VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--skip_fastqc)
|
||||
[ -n "$VIASH_PAR_SKIP_FASTQC" ] && ViashError Bad arguments for option \'--skip_fastqc\': \'$VIASH_PAR_SKIP_FASTQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_SKIP_FASTQC="$2"
|
||||
@@ -1722,17 +1654,6 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_SKIP_MULTIQC=true
|
||||
shift 1
|
||||
;;
|
||||
--extra_fq_subsample_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS" ] && ViashError Bad arguments for option \'--extra_fq_subsample_args\': \'$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_fq_subsample_args. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_fq_subsample_args=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS" ] && ViashError Bad arguments for option \'--extra_fq_subsample_args=*\': \'$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--extra_picard_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_PICARD_ARGS" ] && ViashError Bad arguments for option \'--extra_picard_args\': \'$VIASH_PAR_EXTRA_PICARD_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_PICARD_ARGS="$2"
|
||||
@@ -1744,17 +1665,6 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_EXTRA_PICARD_ARGS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--extra_bedtools_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_BEDTOOLS_ARGS" ] && ViashError Bad arguments for option \'--extra_bedtools_args\': \'$VIASH_PAR_EXTRA_BEDTOOLS_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_BEDTOOLS_ARGS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_bedtools_args. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_bedtools_args=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_BEDTOOLS_ARGS" ] && ViashError Bad arguments for option \'--extra_bedtools_args=*\': \'$VIASH_PAR_EXTRA_BEDTOOLS_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_BEDTOOLS_ARGS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--extra_preseq_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_PRESEQ_ARGS" ] && ViashError Bad arguments for option \'--extra_preseq_args\': \'$VIASH_PAR_EXTRA_PRESEQ_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_PRESEQ_ARGS="$2"
|
||||
@@ -2861,26 +2771,37 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--qualimap_output_pdf)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_OUTPUT_PDF" ] && ViashError Bad arguments for option \'--qualimap_output_pdf\': \'$VIASH_PAR_QUALIMAP_OUTPUT_PDF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_OUTPUT_PDF="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --qualimap_output_pdf. Use "--help" to get more information on the parameters. && exit 1
|
||||
--qualimap_qc_report)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_QC_REPORT" ] && ViashError Bad arguments for option \'--qualimap_qc_report\': \'$VIASH_PAR_QUALIMAP_QC_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_QC_REPORT="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --qualimap_qc_report. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--qualimap_output_pdf=*)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_OUTPUT_PDF" ] && ViashError Bad arguments for option \'--qualimap_output_pdf=*\': \'$VIASH_PAR_QUALIMAP_OUTPUT_PDF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_OUTPUT_PDF=$(ViashRemoveFlags "$1")
|
||||
--qualimap_qc_report=*)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_QC_REPORT" ] && ViashError Bad arguments for option \'--qualimap_qc_report=*\': \'$VIASH_PAR_QUALIMAP_QC_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_QC_REPORT=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--qualimap_output_dir)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--qualimap_output_dir\': \'$VIASH_PAR_QUALIMAP_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_OUTPUT_DIR="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --qualimap_output_dir. Use "--help" to get more information on the parameters. && exit 1
|
||||
--qualimap_counts)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_COUNTS" ] && ViashError Bad arguments for option \'--qualimap_counts\': \'$VIASH_PAR_QUALIMAP_COUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_COUNTS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --qualimap_counts. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--qualimap_output_dir=*)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--qualimap_output_dir=*\': \'$VIASH_PAR_QUALIMAP_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_OUTPUT_DIR=$(ViashRemoveFlags "$1")
|
||||
--qualimap_counts=*)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_COUNTS" ] && ViashError Bad arguments for option \'--qualimap_counts=*\': \'$VIASH_PAR_QUALIMAP_COUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_COUNTS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--qualimap_report)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_REPORT" ] && ViashError Bad arguments for option \'--qualimap_report\': \'$VIASH_PAR_QUALIMAP_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_REPORT="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --qualimap_report. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--qualimap_report=*)
|
||||
[ -n "$VIASH_PAR_QUALIMAP_REPORT" ] && ViashError Bad arguments for option \'--qualimap_report=*\': \'$VIASH_PAR_QUALIMAP_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_QUALIMAP_REPORT=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--deseq2_output)
|
||||
@@ -3227,9 +3148,6 @@ fi
|
||||
if [ -z ${VIASH_PAR_BAM_CSI_INDEX+x} ]; then
|
||||
VIASH_PAR_BAM_CSI_INDEX="false"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_EXTRA_SALMON_QUANT_ARGS+x} ]; then
|
||||
VIASH_PAR_EXTRA_SALMON_QUANT_ARGS="-v"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_MIN_MAPPED_READS+x} ]; then
|
||||
VIASH_PAR_MIN_MAPPED_READS="5"
|
||||
fi
|
||||
@@ -3251,9 +3169,6 @@ fi
|
||||
if [ -z ${VIASH_PAR_SKIP_PSEUDO_ALIGNMENT+x} ]; then
|
||||
VIASH_PAR_SKIP_PSEUDO_ALIGNMENT="false"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS+x} ]; then
|
||||
VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS="--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_SKIP_FASTQC+x} ]; then
|
||||
VIASH_PAR_SKIP_FASTQC="false"
|
||||
fi
|
||||
@@ -3299,15 +3214,9 @@ fi
|
||||
if [ -z ${VIASH_PAR_SKIP_MULTIQC+x} ]; then
|
||||
VIASH_PAR_SKIP_MULTIQC="false"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS+x} ]; then
|
||||
VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS=" --record-count 1000000 --seed 1"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_EXTRA_PICARD_ARGS+x} ]; then
|
||||
VIASH_PAR_EXTRA_PICARD_ARGS=" --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_EXTRA_BEDTOOLS_ARGS+x} ]; then
|
||||
VIASH_PAR_EXTRA_BEDTOOLS_ARGS=" -split -du"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_EXTRA_PRESEQ_ARGS+x} ]; then
|
||||
VIASH_PAR_EXTRA_PRESEQ_ARGS="-verbose -seed 1 -seg_len 100000000"
|
||||
fi
|
||||
@@ -3348,40 +3257,40 @@ if [ -z ${VIASH_PAR_OUTPUT_KALLISTO_INDEX+x} ]; then
|
||||
VIASH_PAR_OUTPUT_KALLISTO_INDEX="reference/index/Kallisto"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_OUTPUT_FASTQ_1+x} ]; then
|
||||
VIASH_PAR_OUTPUT_FASTQ_1="fastq/\$id.read_1.fastq.gz"
|
||||
VIASH_PAR_OUTPUT_FASTQ_1="fastq/\${id}_r1.fastq.gz"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_OUTPUT_FASTQ_2+x} ]; then
|
||||
VIASH_PAR_OUTPUT_FASTQ_2="fastq/\$id.read_2.fastq.gz"
|
||||
VIASH_PAR_OUTPUT_FASTQ_2="fastq/\${id}_r2.fastq.gz"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_FASTQC_HTML_1+x} ]; then
|
||||
VIASH_PAR_FASTQC_HTML_1="fastqc_raw/\$id.read_1.fastqc.html"
|
||||
VIASH_PAR_FASTQC_HTML_1="fastqc_raw/\${id}_r1.fastqc.html"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_FASTQC_HTML_2+x} ]; then
|
||||
VIASH_PAR_FASTQC_HTML_2="fastqc_raw/\$id.read_2.fastqc.html"
|
||||
VIASH_PAR_FASTQC_HTML_2="fastqc_raw/\${id}_r2.fastqc.html"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_FASTQC_ZIP_1+x} ]; then
|
||||
VIASH_PAR_FASTQC_ZIP_1="fastqc_raw/\$id.read_1.fastqc.zip"
|
||||
VIASH_PAR_FASTQC_ZIP_1="fastqc_raw/\${id}_r1.fastqc.zip"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_FASTQC_ZIP_2+x} ]; then
|
||||
VIASH_PAR_FASTQC_ZIP_2="fastqc_raw/\$id.read_2.fastqc.zip"
|
||||
VIASH_PAR_FASTQC_ZIP_2="fastqc_raw/\${id}_r2.fastqc.zip"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_TRIM_HTML_1+x} ]; then
|
||||
VIASH_PAR_TRIM_HTML_1="fastqc_trim/\$id.read_1.trimmed_fastqc.html"
|
||||
VIASH_PAR_TRIM_HTML_1="fastqc_trim/\${id}_r1.trimmed_fastqc.html"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_TRIM_HTML_2+x} ]; then
|
||||
VIASH_PAR_TRIM_HTML_2="fastqc_trim/\$id.read_2.trimmed_fastqc.html"
|
||||
VIASH_PAR_TRIM_HTML_2="fastqc_trim/\${id}_r2.trimmed_fastqc.html"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_TRIM_ZIP_1+x} ]; then
|
||||
VIASH_PAR_TRIM_ZIP_1="fastqc_trim/\$id.read_1.trimmed_fastqc.zip"
|
||||
VIASH_PAR_TRIM_ZIP_1="fastqc_trim/\${id}_r1.trimmed_fastqc.zip"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_TRIM_ZIP_2+x} ]; then
|
||||
VIASH_PAR_TRIM_ZIP_2="fastqc_trim/\$id.read_2.trimmed_fastqc.zip"
|
||||
VIASH_PAR_TRIM_ZIP_2="fastqc_trim/\${id}_r2.trimmed_fastqc.zip"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_TRIM_LOG_1+x} ]; then
|
||||
VIASH_PAR_TRIM_LOG_1="trimgalore/\$id.read_1.trimming_report.txt"
|
||||
VIASH_PAR_TRIM_LOG_1="trimgalore/\${id}_r1.trimming_report.txt"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_TRIM_LOG_2+x} ]; then
|
||||
VIASH_PAR_TRIM_LOG_2="trimgalore/\$id.read_2.trimming_report.txt"
|
||||
VIASH_PAR_TRIM_LOG_2="trimgalore/\${id}_r2.trimming_report.txt"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_FASTP_TRIM_JSON+x} ]; then
|
||||
VIASH_PAR_FASTP_TRIM_JSON="fastp/\$id_out.json"
|
||||
@@ -3605,11 +3514,14 @@ fi
|
||||
if [ -z ${VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE+x} ]; then
|
||||
VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE="dupradar/intercept_slope/\$id.intercept_slope.txt"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_QUALIMAP_OUTPUT_PDF+x} ]; then
|
||||
VIASH_PAR_QUALIMAP_OUTPUT_PDF="qualimap/\$id.qualimap_output.pdf"
|
||||
if [ -z ${VIASH_PAR_QUALIMAP_QC_REPORT+x} ]; then
|
||||
VIASH_PAR_QUALIMAP_QC_REPORT="Qualimap/\$id.rnaseq_qc_results.txt"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_QUALIMAP_OUTPUT_DIR+x} ]; then
|
||||
VIASH_PAR_QUALIMAP_OUTPUT_DIR="qualimap/\$id"
|
||||
if [ -z ${VIASH_PAR_QUALIMAP_COUNTS+x} ]; then
|
||||
VIASH_PAR_QUALIMAP_COUNTS="Qualimap/\$id.counts.txt"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_QUALIMAP_REPORT+x} ]; then
|
||||
VIASH_PAR_QUALIMAP_REPORT="Qualimap/\$id.report.html"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_DESEQ2_OUTPUT+x} ]; then
|
||||
VIASH_PAR_DESEQ2_OUTPUT="deseq2_qc"
|
||||
@@ -3705,9 +3617,17 @@ if [ ! -z "$VIASH_PAR_KALLISTO_INDEX" ] && [ ! -e "$VIASH_PAR_KALLISTO_INDEX" ];
|
||||
ViashError "Input file '$VIASH_PAR_KALLISTO_INDEX' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && [ ! -e "$VIASH_PAR_BBSPLIT_FASTA_LIST" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_BBSPLIT_FASTA_LIST' does not exist."
|
||||
exit 1
|
||||
if [ ! -z "$VIASH_PAR_BBSPLIT_FASTA_LIST" ]; then
|
||||
IFS=';'
|
||||
set -f
|
||||
for file in $VIASH_PAR_BBSPLIT_FASTA_LIST; do
|
||||
unset IFS
|
||||
if [ ! -e "$file" ]; then
|
||||
ViashError "Input file '$file' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
done
|
||||
set +f
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_BBSPLIT_INDEX" ] && [ ! -e "$VIASH_PAR_BBSPLIT_INDEX" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_BBSPLIT_INDEX' does not exist."
|
||||
@@ -3770,14 +3690,14 @@ if [[ -n "$VIASH_PAR_PSEUDO_ALIGNER_KMER_SIZE" ]]; then
|
||||
fi
|
||||
fi
|
||||
if [[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" ]]; then
|
||||
if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
|
||||
ViashError '--kallisto_quant_fragment_length' has to be an integer. Use "--help" to get more information on the parameters.
|
||||
if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
||||
ViashError '--kallisto_quant_fragment_length' has to be a double. Use "--help" to get more information on the parameters.
|
||||
exit 1
|
||||
fi
|
||||
fi
|
||||
if [[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" ]]; then
|
||||
if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" =~ ^[-+]?[0-9]+$ ]]; then
|
||||
ViashError '--kallisto_quant_fragment_length_sd' has to be an integer. Use "--help" to get more information on the parameters.
|
||||
if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
||||
ViashError '--kallisto_quant_fragment_length_sd' has to be a double. Use "--help" to get more information on the parameters.
|
||||
exit 1
|
||||
fi
|
||||
fi
|
||||
@@ -4374,11 +4294,14 @@ fi
|
||||
if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE" ] && [ ! -d "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE")"
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_OUTPUT_PDF" ] && [ ! -d "$(dirname "$VIASH_PAR_QUALIMAP_OUTPUT_PDF")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_QUALIMAP_OUTPUT_PDF")"
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_QC_REPORT" ] && [ ! -d "$(dirname "$VIASH_PAR_QUALIMAP_QC_REPORT")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_QUALIMAP_QC_REPORT")"
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_QUALIMAP_OUTPUT_DIR")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_QUALIMAP_OUTPUT_DIR")"
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_COUNTS" ] && [ ! -d "$(dirname "$VIASH_PAR_QUALIMAP_COUNTS")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_QUALIMAP_COUNTS")"
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_REPORT" ] && [ ! -d "$(dirname "$VIASH_PAR_QUALIMAP_REPORT")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_QUALIMAP_REPORT")"
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_DESEQ2_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_DESEQ2_OUTPUT")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_DESEQ2_OUTPUT")"
|
||||
@@ -4878,8 +4801,9 @@ workflow run_wf {
|
||||
"dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc",
|
||||
"dupradar_output_expression_histogram": "dupradar_output_expression_histogram",
|
||||
"dupradar_output_intercept_slope": "dupradar_output_intercept_slope",
|
||||
"qualimap_output_dir": "qualimap_output_dir",
|
||||
"qualimap_output_pdf": "qualimap_output_pdf",
|
||||
"qualimap_report": "qualimap_report",
|
||||
"qualimap_qc_report": "qualimap_qc_report",
|
||||
"qualimap_counts": "qualimap_counts",
|
||||
"featurecounts": "featurecounts",
|
||||
"featurecounts_summary": "featurecounts_summary",
|
||||
"featurecounts_multiqc": "featurecounts_multiqc",
|
||||
@@ -4993,8 +4917,9 @@ workflow run_wf {
|
||||
"dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc",
|
||||
"dupradar_output_expression_histogram": "dupradar_output_expression_histogram",
|
||||
"dupradar_output_intercept_slope": "dupradar_output_intercept_slope",
|
||||
"qualimap_output_dir": "qualimap_output_dir",
|
||||
"qualimap_output_pdf": "qualimap_output_pdf",
|
||||
"qualimap_report": "qualimap_report",
|
||||
"qualimap_qc_report": "qualimap_qc_report",
|
||||
"qualimap_counts": "qualimap_counts",
|
||||
"tpm_gene": "tpm_gene",
|
||||
"counts_gene": "counts_gene",
|
||||
"counts_gene_length_scaled": "counts_gene_length_scaled",
|
||||
@@ -5418,8 +5343,16 @@ if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE" ] && [ ! -e "$VIASH_PAR_D
|
||||
ViashError "Output file '$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ] && [ ! -e "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ]; then
|
||||
ViashError "Output file '$VIASH_PAR_QUALIMAP_OUTPUT_DIR' does not exist."
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_QC_REPORT" ] && [ ! -e "$VIASH_PAR_QUALIMAP_QC_REPORT" ]; then
|
||||
ViashError "Output file '$VIASH_PAR_QUALIMAP_QC_REPORT' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_COUNTS" ] && [ ! -e "$VIASH_PAR_QUALIMAP_COUNTS" ]; then
|
||||
ViashError "Output file '$VIASH_PAR_QUALIMAP_COUNTS' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_QUALIMAP_REPORT" ] && [ ! -e "$VIASH_PAR_QUALIMAP_REPORT" ]; then
|
||||
ViashError "Output file '$VIASH_PAR_QUALIMAP_REPORT' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_DESEQ2_OUTPUT" ] && [ ! -e "$VIASH_PAR_DESEQ2_OUTPUT" ]; then
|
||||
|
||||
Reference in New Issue
Block a user