vsh/rnaseq
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Build branch main with version main (ce40a4a)

Browse Source 
Build pipeline: viash-hub.rnaseq.main-b6jtr

Source commit: ce40a4a6d9

Source message: add unit tests
This commit is contained in:
CI
2024-11-27 09:19:16 +00:00
parent 20fef7a87e
commit 14e0d12189
295 changed files with 8300 additions and 8134 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
target/executable/bbmap_bbsplit/.config.vsh.yaml
View File

@@ -238,8 +238,8 @@ build_info:
output: "target/executable/bbmap_bbsplit"
executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/bbmap_bbsplit/bbmap_bbsplit
View File

@@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \
cp -r bbmap/* /usr/local/bin
LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit"
LABEL org.opencontainers.image.created="2024-11-21T08:06:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/bedtools_genomecov/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/bedtools_genomecov/bedtools_genomecov
View File

@@ -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="2024-11-21T08:06:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/cat_additional_fasta/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/cat_additional_fasta/cat_additional_fasta
View File

@@ -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="2024-11-21T08:06:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/cat_fastq/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/cat_fastq/cat_fastq
View File

@@ -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="2024-11-21T08:06:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/deseq2_qc/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/deseq2_qc/deseq2_qc
View File

@@ -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="2024-11-21T08:06:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/dupradar/.config.vsh.yaml
View File

@@ -266,8 +266,8 @@ build_info:
output: "target/executable/dupradar"
executable: "target/executable/dupradar/dupradar"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/dupradar/dupradar
View File

@@ -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="2024-11-21T08:06:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/fastqc/.config.vsh.yaml
View File

@@ -198,8 +198,8 @@ build_info:
output: "target/executable/fastqc"
executable: "target/executable/fastqc/fastqc"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/fastqc/fastqc
View File

@@ -490,9 +490,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component fastqc"
LABEL org.opencontainers.image.created="2024-11-21T08:06:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/fq_subsample/.config.vsh.yaml
View File

@@ -177,8 +177,8 @@ build_info:
output: "target/executable/fq_subsample"
executable: "target/executable/fq_subsample/fq_subsample"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/fq_subsample/fq_subsample
View File

@@ -485,9 +485,9 @@ cargo install --locked --path . && \
mv /usr/local/fq/target/release/fq /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
LABEL org.opencontainers.image.created="2024-11-21T08:06:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/getchromsizes/.config.vsh.yaml
View File

@@ -167,8 +167,8 @@ build_info:
output: "target/executable/getchromsizes"
executable: "target/executable/getchromsizes/getchromsizes"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/getchromsizes/getchromsizes
View File

@@ -480,9 +480,9 @@ make && \
make install
LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
LABEL org.opencontainers.image.created="2024-11-21T08:06:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/gtf2bed/.config.vsh.yaml
View File

@@ -145,8 +145,8 @@ build_info:
output: "target/executable/gtf2bed"
executable: "target/executable/gtf2bed/gtf2bed"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/gtf2bed/gtf2bed
View File

@@ -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="2024-11-21T08:06:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/gtf_filter/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/gtf_filter/gtf_filter
View File

@@ -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="2024-11-21T08:06:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/gunzip/.config.vsh.yaml
View File

@@ -144,8 +144,8 @@ build_info:
output: "target/executable/gunzip"
executable: "target/executable/gunzip/gunzip"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/gunzip/gunzip
View File

@@ -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="2024-11-21T08:05:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/kallisto/kallisto_index/.config.vsh.yaml
View File

@@ -155,8 +155,8 @@ build_info:
output: "target/executable/kallisto/kallisto_index"
executable: "target/executable/kallisto/kallisto_index/kallisto_index"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/kallisto/kallisto_index/kallisto_index
View File

@@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
LABEL org.opencontainers.image.created="2024-11-21T08:06:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
LABEL org.opencontainers.image.created="2024-11-27T08:42:25Z"
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.version="main"
VIASHDOCKER

4
target/executable/kallisto/kallisto_quant/.config.vsh.yaml
View File

@@ -253,8 +253,8 @@ build_info:
output: "target/executable/kallisto/kallisto_quant"
executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/kallisto/kallisto_quant/kallisto_quant
View File

@@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
LABEL org.opencontainers.image.created="2024-11-21T08:06:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
LABEL org.opencontainers.image.created="2024-11-27T08:42:25Z"
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.version="main"
VIASHDOCKER

8
target/executable/multiqc_custom_biotype/.config.vsh.yaml
View File

@@ -64,6 +64,10 @@ resources:
- type: "file"
path: "biotypes_header.txt"
description: "Calculate features percentage for biotype counts"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info: null
status: "enabled"
requirements:
@@ -161,8 +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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

8
target/executable/multiqc_custom_biotype/multiqc_custom_biotype
View File

@@ -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="2024-11-21T08:06:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER
@@ -1183,7 +1183,7 @@ if __name__ == "__main__":
filtered_lines.append(filtered_line)
# Concatenate the header and the processed lines
result = biotypes_header + '\\n' + '\\n'.join(filtered_lines) + '\\n'
result = biotypes_header + '\\n'.join(filtered_lines) + '\\n'
# Write the result to par_featurecounts_multiqc
with open(par["featurecounts_multiqc"], 'w') as output_file:

4
target/executable/picard_markduplicates/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/picard_markduplicates/picard_markduplicates
View File

@@ -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="2024-11-21T08:06:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/prepare_multiqc_input/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/prepare_multiqc_input/prepare_multiqc_input
View File

@@ -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="2024-11-21T08:05:57Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
View File

@@ -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="2024-11-21T08:06:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/preseq_lcextrap/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/preseq_lcextrap/preseq_lcextrap
View File

@@ -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="2024-11-21T08:06:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/qualimap/.config.vsh.yaml
View File

@@ -271,8 +271,8 @@ build_info:
output: "target/executable/qualimap"
executable: "target/executable/qualimap/qualimap"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/qualimap/qualimap
View File

@@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component qualimap"
LABEL org.opencontainers.image.created="2024-11-21T08:05:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
View File

@@ -299,8 +299,8 @@ build_info:
output: "target/executable/rsem/rsem_calculate_expression"
executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
View File

@@ -542,9 +542,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \
/bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR"
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
LABEL org.opencontainers.image.created="2024-11-21T08:05:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
View File

@@ -182,8 +182,8 @@ build_info:
output: "target/executable/rsem/rsem_merge_counts"
executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/rsem/rsem_merge_counts/rsem_merge_counts
View File

@@ -483,9 +483,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts"
LABEL org.opencontainers.image.created="2024-11-21T08:05:58Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
View File

@@ -163,8 +163,8 @@ build_info:
output: "target/executable/rseqc/rseqc_bamstat"
executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
View File

@@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat"
LABEL org.opencontainers.image.created="2024-11-21T08:06:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
View File

@@ -186,8 +186,8 @@ build_info:
output: "target/executable/rseqc/rseqc_inferexperiment"
executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
View File

@@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment"
LABEL org.opencontainers.image.created="2024-11-21T08:06:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
View File

@@ -272,8 +272,8 @@ build_info:
output: "target/executable/rseqc/rseqc_innerdistance"
executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
View File

@@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance"
LABEL org.opencontainers.image.created="2024-11-21T08:06:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation
View File

@@ -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="2024-11-21T08:06:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation
View File

@@ -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="2024-11-21T08:06:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution
View File

@@ -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="2024-11-21T08:06:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/rseqc/rseqc_readduplication/rseqc_readduplication
View File

@@ -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="2024-11-21T08:06:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_tin/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/rseqc/rseqc_tin/rseqc_tin
View File

@@ -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="2024-11-21T08:06:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/sortmerna/.config.vsh.yaml
View File

@@ -192,8 +192,8 @@ build_info:
output: "target/executable/sortmerna"
executable: "target/executable/sortmerna/sortmerna"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/sortmerna/sortmerna
View File

@@ -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="2024-11-21T08:06:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/stringtie/.config.vsh.yaml
View File

@@ -216,8 +216,8 @@ build_info:
output: "target/executable/stringtie"
executable: "target/executable/stringtie/stringtie"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/stringtie/stringtie
View File

@@ -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="2024-11-21T08:06:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/summarizedexperiment/.config.vsh.yaml
View File

@@ -199,8 +199,8 @@ build_info:
output: "target/executable/summarizedexperiment"
executable: "target/executable/summarizedexperiment/summarizedexperiment"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/summarizedexperiment/summarizedexperiment
View File

@@ -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="2024-11-21T08:06:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/trimgalore/.config.vsh.yaml
View File

@@ -788,8 +788,8 @@ build_info:
output: "target/executable/trimgalore"
executable: "target/executable/trimgalore/trimgalore"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/executable/trimgalore/trimgalore
View File

@@ -858,9 +858,9 @@ ENTRYPOINT []
RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component trimgalore"
LABEL org.opencontainers.image.created="2024-11-21T08:06:07Z"
LABEL org.opencontainers.image.created="2024-11-27T08:42:32Z"
LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

21
target/executable/tx2gene/.config.vsh.yaml
View File

@@ -11,7 +11,7 @@ argument_groups:
required: false
direction: "input"
multiple: true
multiple_sep: ","
multiple_sep: ";"
- type: "file"
name: "--gtf"
info: null
@@ -63,17 +63,6 @@ argument_groups:
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--updated_versions"
info: null
default:
- "versions.yml"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
@@ -81,6 +70,10 @@ resources:
- type: "file"
path: "tx2gene.py"
description: "Get transcript id (tx) to gene names for tximport"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info:
migration_info:
git_repo: "https://github.com/nf-core/rnaseq.git"
@@ -192,8 +185,8 @@ build_info:
output: "target/executable/tx2gene"
executable: "target/executable/tx2gene/tx2gene"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

60
target/executable/tx2gene/tx2gene
View File

@@ -199,10 +199,6 @@ function ViashHelp {
echo " --tsv"
echo " type: file, output, file must exist"
echo " default: tx2gene.tsv"
echo ""
echo " --updated_versions"
echo " type: file, output, file must exist"
echo " default: versions.yml"
}
# initialise variables
@@ -487,9 +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="2024-11-21T08:06:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER
@@ -633,7 +629,7 @@ while [[ $# -gt 0 ]]; do
if [ -z "$VIASH_PAR_QUANT_RESULTS" ]; then
VIASH_PAR_QUANT_RESULTS="$2"
else
VIASH_PAR_QUANT_RESULTS="$VIASH_PAR_QUANT_RESULTS,""$2"
VIASH_PAR_QUANT_RESULTS="$VIASH_PAR_QUANT_RESULTS;""$2"
fi
[ $# -lt 2 ] && ViashError Not enough arguments passed to --quant_results. Use "--help" to get more information on the parameters. && exit 1
shift 2
@@ -642,7 +638,7 @@ while [[ $# -gt 0 ]]; do
if [ -z "$VIASH_PAR_QUANT_RESULTS" ]; then
VIASH_PAR_QUANT_RESULTS=$(ViashRemoveFlags "$1")
else
VIASH_PAR_QUANT_RESULTS="$VIASH_PAR_QUANT_RESULTS,"$(ViashRemoveFlags "$1")
VIASH_PAR_QUANT_RESULTS="$VIASH_PAR_QUANT_RESULTS;"$(ViashRemoveFlags "$1")
fi
shift 1
;;
@@ -701,17 +697,6 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_TSV=$(ViashRemoveFlags "$1")
shift 1
;;
--updated_versions)
[ -n "$VIASH_PAR_UPDATED_VERSIONS" ] && ViashError Bad arguments for option \'--updated_versions\': \'$VIASH_PAR_UPDATED_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_UPDATED_VERSIONS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --updated_versions. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--updated_versions=*)
[ -n "$VIASH_PAR_UPDATED_VERSIONS" ] && ViashError Bad arguments for option \'--updated_versions=*\': \'$VIASH_PAR_UPDATED_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_UPDATED_VERSIONS=$(ViashRemoveFlags "$1")
shift 1
;;
---engine)
VIASH_ENGINE_ID="$2"
shift 2
@@ -919,13 +904,10 @@ fi
if [ -z ${VIASH_PAR_TSV+x} ]; then
VIASH_PAR_TSV="tx2gene.tsv"
fi
if [ -z ${VIASH_PAR_UPDATED_VERSIONS+x} ]; then
VIASH_PAR_UPDATED_VERSIONS="versions.yml"
fi
# check whether required files exist
if [ ! -z "$VIASH_PAR_QUANT_RESULTS" ]; then
IFS=','
IFS=';'
set -f
for file in $VIASH_PAR_QUANT_RESULTS; do
unset IFS
@@ -1032,9 +1014,6 @@ fi
if [ ! -z "$VIASH_PAR_TSV" ] && [ ! -d "$(dirname "$VIASH_PAR_TSV")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_TSV")"
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_UPDATED_VERSIONS")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_UPDATED_VERSIONS")"
fi
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
if [ "$VIASH_MODE" == "run" ]; then
@@ -1050,14 +1029,14 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_QUANT_RESULTS" ]; then
VIASH_TEST_QUANT_RESULTS=()
IFS=','
IFS=';'
for var in $VIASH_PAR_QUANT_RESULTS; do
unset IFS
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
var=$(ViashDockerAutodetectMount "$var")
VIASH_TEST_QUANT_RESULTS+=( "$var" )
done
VIASH_PAR_QUANT_RESULTS=$(IFS=',' ; echo "${VIASH_TEST_QUANT_RESULTS[*]}")
VIASH_PAR_QUANT_RESULTS=$(IFS=';' ; echo "${VIASH_TEST_QUANT_RESULTS[*]}")
fi
if [ ! -z "$VIASH_PAR_GTF" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GTF")" )
@@ -1068,11 +1047,6 @@ if [ ! -z "$VIASH_PAR_TSV" ]; then
VIASH_PAR_TSV=$(ViashDockerAutodetectMount "$VIASH_PAR_TSV")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_TSV" )
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_UPDATED_VERSIONS")" )
VIASH_PAR_UPDATED_VERSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_UPDATED_VERSIONS")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_UPDATED_VERSIONS" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
@@ -1148,7 +1122,6 @@ $( if [ ! -z ${VIASH_PAR_GTF_EXTRA_ATTRIBUTES+x} ]; then echo "${VIASH_PAR_GTF_E
$( if [ ! -z ${VIASH_PAR_GTF_GROUP_FEATURES+x} ]; then echo "${VIASH_PAR_GTF_GROUP_FEATURES}" | sed "s#'#'\"'\"'#g;s#.*#par_gtf_group_features='&'#" ; else echo "# par_gtf_group_features="; fi )
$( if [ ! -z ${VIASH_PAR_QUANT_TYPE+x} ]; then echo "${VIASH_PAR_QUANT_TYPE}" | sed "s#'#'\"'\"'#g;s#.*#par_quant_type='&'#" ; else echo "# par_quant_type="; fi )
$( if [ ! -z ${VIASH_PAR_TSV+x} ]; then echo "${VIASH_PAR_TSV}" | sed "s#'#'\"'\"'#g;s#.*#par_tsv='&'#" ; else echo "# par_tsv="; fi )
$( if [ ! -z ${VIASH_PAR_UPDATED_VERSIONS+x} ]; then echo "${VIASH_PAR_UPDATED_VERSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_updated_versions='&'#" ; else echo "# par_updated_versions="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
@@ -1174,13 +1147,13 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
set -eo pipefail
function clean_up {
rm -rf "\$salmon_tmpdir"
rm -rf "\$tmpdir"
}
trap clean_up EXIT
tmpdir=\$(mktemp -d "\$meta_temp_dir/\$meta_functionality_name-XXXXXXXX")
tmpdir=\$(mktemp -d "\$meta_temp_dir/\$meta_name-XXXXXXXX")
IFS="," read -ra results <<< \$par_quant_results
IFS=";" read -ra results <<< \$par_quant_results
for result in \${results[*]}
do
cp -r \$result \$tmpdir
@@ -1205,13 +1178,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_QUANT_RESULTS" ]; then
unset VIASH_TEST_QUANT_RESULTS
IFS=','
IFS=';'
for var in $VIASH_PAR_QUANT_RESULTS; do
unset IFS
if [ -z "$VIASH_TEST_QUANT_RESULTS" ]; then
VIASH_TEST_QUANT_RESULTS="$(ViashDockerStripAutomount "$var")"
else
VIASH_TEST_QUANT_RESULTS="$VIASH_TEST_QUANT_RESULTS,""$(ViashDockerStripAutomount "$var")"
VIASH_TEST_QUANT_RESULTS="$VIASH_TEST_QUANT_RESULTS;""$(ViashDockerStripAutomount "$var")"
fi
done
VIASH_PAR_QUANT_RESULTS="$VIASH_TEST_QUANT_RESULTS"
@@ -1222,9 +1195,6 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_TSV" ]; then
VIASH_PAR_TSV=$(ViashDockerStripAutomount "$VIASH_PAR_TSV")
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ]; then
VIASH_PAR_UPDATED_VERSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_UPDATED_VERSIONS")
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
fi
@@ -1245,10 +1215,6 @@ if [ ! -z "$VIASH_PAR_TSV" ] && [ ! -e "$VIASH_PAR_TSV" ]; then
ViashError "Output file '$VIASH_PAR_TSV' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ] && [ ! -e "$VIASH_PAR_UPDATED_VERSIONS" ]; then
ViashError "Output file '$VIASH_PAR_UPDATED_VERSIONS' does not exist."
exit 1
fi
exit 0

14
target/executable/tximport/.config.vsh.yaml
View File

@@ -11,7 +11,7 @@ argument_groups:
required: false
direction: "input"
multiple: true
multiple_sep: ","
multiple_sep: ";"
- type: "file"
name: "--tx2gene_tsv"
info: null
@@ -82,7 +82,7 @@ argument_groups:
name: "--lengths_gene"
info: null
default:
- "merged.gene_length.tsv"
- "merged.gene_lengths.tsv"
must_exist: true
create_parent: true
required: false
@@ -115,7 +115,7 @@ argument_groups:
name: "--lengths_transcript"
info: null
default:
- "merged.transcript_length.tsv"
- "merged.transcript_lengths.tsv"
must_exist: true
create_parent: true
required: false
@@ -129,6 +129,10 @@ resources:
- type: "file"
path: "tximport.r"
description: "Get dataframe linking transcript ID, gene ID, and gene name"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info:
migration_info:
git_repo: "https://github.com/nf-core/rnaseq.git"
@@ -247,8 +251,8 @@ build_info:
output: "target/executable/tximport"
executable: "target/executable/tximport/tximport"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

34
target/executable/tximport/tximport
View File

@@ -206,7 +206,7 @@ function ViashHelp {
echo ""
echo " --lengths_gene"
echo " type: file, output, file must exist"
echo " default: merged.gene_length.tsv"
echo " default: merged.gene_lengths.tsv"
echo ""
echo " --tpm_transcript"
echo " type: file, output, file must exist"
@@ -218,7 +218,7 @@ function ViashHelp {
echo ""
echo " --lengths_transcript"
echo " type: file, output, file must exist"
echo " default: merged.transcript_length.tsv"
echo " default: merged.transcript_lengths.tsv"
}
# initialise variables
@@ -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="2024-11-21T08:06:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER
@@ -654,7 +654,7 @@ while [[ $# -gt 0 ]]; do
if [ -z "$VIASH_PAR_QUANT_RESULTS" ]; then
VIASH_PAR_QUANT_RESULTS="$2"
else
VIASH_PAR_QUANT_RESULTS="$VIASH_PAR_QUANT_RESULTS,""$2"
VIASH_PAR_QUANT_RESULTS="$VIASH_PAR_QUANT_RESULTS;""$2"
fi
[ $# -lt 2 ] && ViashError Not enough arguments passed to --quant_results. Use "--help" to get more information on the parameters. && exit 1
shift 2
@@ -663,7 +663,7 @@ while [[ $# -gt 0 ]]; do
if [ -z "$VIASH_PAR_QUANT_RESULTS" ]; then
VIASH_PAR_QUANT_RESULTS=$(ViashRemoveFlags "$1")
else
VIASH_PAR_QUANT_RESULTS="$VIASH_PAR_QUANT_RESULTS,"$(ViashRemoveFlags "$1")
VIASH_PAR_QUANT_RESULTS="$VIASH_PAR_QUANT_RESULTS;"$(ViashRemoveFlags "$1")
fi
shift 1
;;
@@ -988,7 +988,7 @@ if [ -z ${VIASH_PAR_COUNTS_GENE_SCALED+x} ]; then
VIASH_PAR_COUNTS_GENE_SCALED="merged.gene_counts_scaled.tsv"
fi
if [ -z ${VIASH_PAR_LENGTHS_GENE+x} ]; then
VIASH_PAR_LENGTHS_GENE="merged.gene_length.tsv"
VIASH_PAR_LENGTHS_GENE="merged.gene_lengths.tsv"
fi
if [ -z ${VIASH_PAR_TPM_TRANSCRIPT+x} ]; then
VIASH_PAR_TPM_TRANSCRIPT="merged.transcript_tpm.tsv"
@@ -997,12 +997,12 @@ if [ -z ${VIASH_PAR_COUNTS_TRANSCRIPT+x} ]; then
VIASH_PAR_COUNTS_TRANSCRIPT="merged.transcript_counts.tsv"
fi
if [ -z ${VIASH_PAR_LENGTHS_TRANSCRIPT+x} ]; then
VIASH_PAR_LENGTHS_TRANSCRIPT="merged.transcript_length.tsv"
VIASH_PAR_LENGTHS_TRANSCRIPT="merged.transcript_lengths.tsv"
fi
# check whether required files exist
if [ ! -z "$VIASH_PAR_QUANT_RESULTS" ]; then
IFS=','
IFS=';'
set -f
for file in $VIASH_PAR_QUANT_RESULTS; do
unset IFS
@@ -1145,14 +1145,14 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_QUANT_RESULTS" ]; then
VIASH_TEST_QUANT_RESULTS=()
IFS=','
IFS=';'
for var in $VIASH_PAR_QUANT_RESULTS; do
unset IFS
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
var=$(ViashDockerAutodetectMount "$var")
VIASH_TEST_QUANT_RESULTS+=( "$var" )
done
VIASH_PAR_QUANT_RESULTS=$(IFS=',' ; echo "${VIASH_TEST_QUANT_RESULTS[*]}")
VIASH_PAR_QUANT_RESULTS=$(IFS=';' ; echo "${VIASH_TEST_QUANT_RESULTS[*]}")
fi
if [ ! -z "$VIASH_PAR_TX2GENE_TSV" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_TX2GENE_TSV")" )
@@ -1303,13 +1303,13 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
set -eo pipefail
function clean_up {
rm -rf "\$salmon_tmpdir"
rm -rf "\$tmpdir"
}
trap clean_up EXIT
tmpdir=\$(mktemp -d "\$meta_temp_dir/\$meta_functionality_name-XXXXXXXX")
tmpdir=\$(mktemp -d "\$meta_temp_dir/\$meta_name-XXXXXXXX")
IFS="," read -ra results <<< \$par_quant_results
IFS=";" read -ra results <<< \$par_quant_results
for result in \${results[*]}
do
cp -r \$result \$tmpdir
@@ -1333,13 +1333,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_QUANT_RESULTS" ]; then
unset VIASH_TEST_QUANT_RESULTS
IFS=','
IFS=';'
for var in $VIASH_PAR_QUANT_RESULTS; do
unset IFS
if [ -z "$VIASH_TEST_QUANT_RESULTS" ]; then
VIASH_TEST_QUANT_RESULTS="$(ViashDockerStripAutomount "$var")"
else
VIASH_TEST_QUANT_RESULTS="$VIASH_TEST_QUANT_RESULTS,""$(ViashDockerStripAutomount "$var")"
VIASH_TEST_QUANT_RESULTS="$VIASH_TEST_QUANT_RESULTS;""$(ViashDockerStripAutomount "$var")"
fi
done
VIASH_PAR_QUANT_RESULTS="$VIASH_TEST_QUANT_RESULTS"

4
target/executable/ucsc/bedclip/.config.vsh.yaml
View File

@@ -164,8 +164,8 @@ build_info:
output: "target/executable/ucsc/bedclip"
executable: "target/executable/ucsc/bedclip/bedclip"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/ucsc/bedclip/bedclip
View File

@@ -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="2024-11-21T08:06:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml
View File

@@ -164,8 +164,8 @@ build_info:
output: "target/executable/ucsc/bedgraphtobigwig"
executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig
View File

@@ -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="2024-11-21T08:06:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/umitools/umitools_dedup/.config.vsh.yaml
View File

@@ -195,8 +195,8 @@ build_info:
output: "target/executable/umitools/umitools_dedup"
executable: "target/executable/umitools/umitools_dedup/umitools_dedup"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/umitools/umitools_dedup/umitools_dedup
View File

@@ -489,9 +489,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools"
LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup"
LABEL org.opencontainers.image.created="2024-11-21T08:06:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

4
target/executable/umitools/umitools_extract/.config.vsh.yaml
View File

@@ -253,8 +253,8 @@ build_info:
output: "target/executable/umitools/umitools_extract"
executable: "target/executable/umitools/umitools_extract/umitools_extract"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/umitools/umitools_extract/umitools_extract
View File

@@ -521,9 +521,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools"
LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract"
LABEL org.opencontainers.image.created="2024-11-21T08:06:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
LABEL org.opencontainers.image.created="2024-11-27T08:42:25Z"
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.version="main"
VIASHDOCKER

4
target/executable/umitools_prepareforquant/.config.vsh.yaml
View File

@@ -156,8 +156,8 @@ build_info:
output: "target/executable/umitools_prepareforquant"
executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/umitools_prepareforquant/umitools_prepareforquant
View File

@@ -473,9 +473,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools" "pysam"
LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant"
LABEL org.opencontainers.image.created="2024-11-21T08:06:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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.version="main"
VIASHDOCKER

27
target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
View File

@@ -93,32 +93,13 @@ argument_groups:
multiple: false
multiple_sep: ";"
- type: "string"
name: "--seq_platform"
description: "Sequencing platform."
name: "--star_sjdb_gtf_feature_exon"
description: "Feature type in GTF file to be used as exons for building transcripts"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--seq_center"
description: "Sequencing center."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--extra_star_align_args"
description: "Extra arguments to pass to STAR alignment 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\
@@ -603,8 +584,8 @@ 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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@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"

768
target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant
View File

@@ -215,19 +215,9 @@ function ViashHelp {
echo " When using pre-built STAR indices do not re-extract and use splice"
echo " junctions from the GTF file"
echo ""
echo " --seq_platform"
echo " --star_sjdb_gtf_feature_exon"
echo " type: string"
echo " Sequencing platform."
echo ""
echo " --seq_center"
echo " type: string"
echo " Sequencing center."
echo ""
echo " --extra_star_align_args"
echo " type: string"
echo " default:"
echo " Extra arguments to pass to STAR alignment command in addition to"
echo " defaults defined by the pipeline."
echo " Feature type in GTF file to be used as exons for building transcripts"
echo ""
echo " --bam_csi_index"
echo " type: boolean"
@@ -498,37 +488,15 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_STAR_IGNORE_SJDBGTF=$(ViashRemoveFlags "$1")
shift 1
;;
--seq_platform)
[ -n "$VIASH_PAR_SEQ_PLATFORM" ] && ViashError Bad arguments for option \'--seq_platform\': \'$VIASH_PAR_SEQ_PLATFORM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SEQ_PLATFORM="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --seq_platform. Use "--help" to get more information on the parameters. && exit 1
--star_sjdb_gtf_feature_exon)
[ -n "$VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON" ] && ViashError Bad arguments for option \'--star_sjdb_gtf_feature_exon\': \'$VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --star_sjdb_gtf_feature_exon. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--seq_platform=*)
[ -n "$VIASH_PAR_SEQ_PLATFORM" ] && ViashError Bad arguments for option \'--seq_platform=*\': \'$VIASH_PAR_SEQ_PLATFORM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SEQ_PLATFORM=$(ViashRemoveFlags "$1")
shift 1
;;
--seq_center)
[ -n "$VIASH_PAR_SEQ_CENTER" ] && ViashError Bad arguments for option \'--seq_center\': \'$VIASH_PAR_SEQ_CENTER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SEQ_CENTER="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --seq_center. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--seq_center=*)
[ -n "$VIASH_PAR_SEQ_CENTER" ] && ViashError Bad arguments for option \'--seq_center=*\': \'$VIASH_PAR_SEQ_CENTER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SEQ_CENTER=$(ViashRemoveFlags "$1")
shift 1
;;
--extra_star_align_args)
[ -n "$VIASH_PAR_EXTRA_STAR_ALIGN_ARGS" ] && ViashError Bad arguments for option \'--extra_star_align_args\': \'$VIASH_PAR_EXTRA_STAR_ALIGN_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_EXTRA_STAR_ALIGN_ARGS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_star_align_args. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--extra_star_align_args=*)
[ -n "$VIASH_PAR_EXTRA_STAR_ALIGN_ARGS" ] && ViashError Bad arguments for option \'--extra_star_align_args=*\': \'$VIASH_PAR_EXTRA_STAR_ALIGN_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_EXTRA_STAR_ALIGN_ARGS=$(ViashRemoveFlags "$1")
--star_sjdb_gtf_feature_exon=*)
[ -n "$VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON" ] && ViashError Bad arguments for option \'--star_sjdb_gtf_feature_exon=*\': \'$VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON=$(ViashRemoveFlags "$1")
shift 1
;;
--bam_csi_index)
@@ -1012,9 +980,6 @@ fi
if [ -z ${VIASH_PAR_STAR_IGNORE_SJDBGTF+x} ]; then
VIASH_PAR_STAR_IGNORE_SJDBGTF="false"
fi
if [ -z ${VIASH_PAR_EXTRA_STAR_ALIGN_ARGS+x} ]; then
VIASH_PAR_EXTRA_STAR_ALIGN_ARGS=""
fi
if [ -z ${VIASH_PAR_BAM_CSI_INDEX+x} ]; then
VIASH_PAR_BAM_CSI_INDEX="false"
fi
@@ -1355,381 +1320,382 @@ workflow run_wf {
main:
output_ch = input_ch
| map { id, state ->
def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
def paired = input.size() == 2
[ id, state + [ paired: paired, input: input ] ]
}
| map { id, state ->
def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
def paired = input.size() == 2
[ id, state + [ paired: paired, input: input ] ]
}
| star_align_reads.run (
runIf: { id, state -> state.aligner == 'star_salmon' },
fromState: [
"input": "fastq_1",
"input_r2": "fastq_2",
"genome_dir": "star_index",
"sjdb_gtf_file": "gtf",
"out_sam_attr_rg_line": "star_sam_attr_rg_line"
],
toState: [
"genome_bam": "aligned_reads",
"transcriptome_bam": "reads_aligned_to_transcriptome",
"star_multiqc": "log"
],
args: [
quant_mode: "TranscriptomeSAM",
twopass_mode: "Basic",
out_sam_type: "BAM;Unsorted",
run_rng_seed: 0,
out_filter_multimap_nmax: 20,
align_sjdb_overhang_min: 1,
out_sam_attributes: "NH;HI;AS;NM;MD",
quant_transcriptome_sam_output: "BanSingleEnd"
]
)
| star_align_reads.run (
runIf: { id, state -> state.aligner == 'star_salmon' },
fromState: [
"input": "fastq_1",
"input_r2": "fastq_2",
"genome_dir": "star_index",
"sjdb_gtf_file": "gtf",
"out_sam_attr_rg_line": "star_sam_attr_rg_line",
"sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon"
],
toState: [
"genome_bam": "aligned_reads",
"transcriptome_bam": "reads_aligned_to_transcriptome",
"star_multiqc": "log"
],
args: [
quant_mode: "TranscriptomeSAM",
twopass_mode: "Basic",
out_sam_type: "BAM;Unsorted",
run_rng_seed: 0,
out_filter_multimap_nmax: 20,
align_sjdb_overhang_min: 1,
out_sam_attributes: "NH;HI;AS;NM;MD",
quant_transcriptome_sam_output: "BanSingleEnd"
]
)
// GENOME BAM
| samtools_sort.run (
runIf: { id, state -> state.aligner == 'star_salmon' },
fromState: ["input": "genome_bam"],
toState: ["genome_bam_sorted": "output"],
key: "genome_sorted"
)
| samtools_index.run (
runIf: { id, state -> state.aligner == 'star_salmon' },
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_salmon' },
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_salmon' },
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_salmon' },
fromState: [
"bam": "genome_bam_sorted",
"bai": "genome_bam_index",
"fasta": "fasta"
],
toState: [ "genome_bam_idxstats": "output" ],
key: "genome_idxstats"
)
// GENOME BAM
| samtools_sort.run (
runIf: { id, state -> state.aligner == 'star_salmon' },
fromState: ["input": "genome_bam"],
toState: ["genome_bam_sorted": "output"],
key: "genome_sorted"
)
| samtools_index.run (
runIf: { id, state -> state.aligner == 'star_salmon' },
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_salmon' },
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_salmon' },
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_salmon' },
fromState: [
"bam": "genome_bam_sorted",
"bai": "genome_bam_index",
"fasta": "fasta"
],
toState: [ "genome_bam_idxstats": "output" ],
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
| 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"
)
// Deduplicate transcriptome BAM file
// 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 (
| 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 (
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 (
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"
)
)
| 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
| umitools_prepareforquant.run (
runIf: { id, state -> state.with_umi && state.paired && state.aligner == 'star_salmon' },
fromState: [ "bam": "transcriptome_bam" ],
toState: [ "transcriptome_bam": "output" ]
)
// Infer lib-type for salmon quant
| map { id, state ->
def lib_type = (state.paired) ?
(
(state.strandedness == "forward") ?
"ISF" :
(
(state.strandedness == "reverse") ? "ISR" : "IU"
)
)
: (
(state.strandedness == "forward") ?
"SF" :
(
(state.strandedness == "reverse") ? "SR" : "U"
)
)
[ id, state + [lib_type: lib_type] ]
}
// Infer lib-type for salmon quant
| map { id, state ->
def lib_type = (state.paired) ?
(
(state.strandedness == "forward") ?
"ISF" :
(
(state.strandedness == "reverse") ? "ISR" : "IU"
)
)
: (
(state.strandedness == "forward") ?
"SF" :
(
(state.strandedness == "reverse") ? "SR" : "U"
)
)
[ id, state + [lib_type: lib_type] ]
}
// Count reads from BAM alignments using Salmon
| salmon_quant.run (
runIf: { id, state -> state.aligner == 'star_salmon' },
fromState: [
"lib_type": "lib_type",
"alignments": "transcriptome_bam",
"targets": "transcript_fasta",
"gene_map": "gtf"
],
toState: [
"quant_out_dir": "output",
"quant_results_file": "quant_results"
]
)
// Count reads from BAM alignments using Salmon
| salmon_quant.run (
runIf: { id, state -> state.aligner == 'star_salmon' },
fromState: [
"lib_type": "lib_type",
"alignments": "transcriptome_bam",
"targets": "transcript_fasta",
"gene_map": "gtf"
],
toState: [
"quant_out_dir": "output",
"quant_results_file": "quant_results"
]
)
| 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",
"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.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 (
[ "star_multiqc": "star_multiqc",
"rsem_multiqc": "rsem_multiqc",
"salmon_multiqc": "salmon_multiqc",
"genome_bam_sorted": "genome_bam_sorted",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"transcriptome_bam": "transcriptome_bam",
"transcriptome_bam_index": "transcriptome_bam_index",
"transcriptome_bam_stats": "transcriptome_bam_stats",
"transcriptome_bam_flagstat": "transcriptome_bam_flagstat",
"transcriptome_bam_idxstats": "transcriptome_bam_idxstats",
"quant_out_dir": "quant_out_dir",
"quant_results_file": "quant_results_file",
"rsem_counts_gene": "rsem_counts_gene",
"rsem_counts_transcripts": "rsem_counts_transcripts",
"bam_genome_rsem": "bam_genome_rsem",
"bam_transcript_rsem": "bam_transcript_rsem" ]
)
| setState (
[ "star_multiqc": "star_multiqc",
"rsem_multiqc": "rsem_multiqc",
"salmon_multiqc": "salmon_multiqc",
"genome_bam_sorted": "genome_bam_sorted",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"transcriptome_bam": "transcriptome_bam",
"transcriptome_bam_index": "transcriptome_bam_index",
"transcriptome_bam_stats": "transcriptome_bam_stats",
"transcriptome_bam_flagstat": "transcriptome_bam_flagstat",
"transcriptome_bam_idxstats": "transcriptome_bam_idxstats",
"quant_out_dir": "quant_out_dir",
"quant_results_file": "quant_results_file",
"rsem_counts_gene": "rsem_counts_gene",
"rsem_counts_transcripts": "rsem_counts_transcripts",
"bam_genome_rsem": "bam_genome_rsem",
"bam_transcript_rsem": "bam_transcript_rsem" ]
)
emit:
output_ch

4
target/executable/workflows/merge_quant_results/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/tx2gene"
- "target/nextflow/tximport"

100
target/executable/workflows/merge_quant_results/merge_quant_results
View File

@@ -783,62 +783,62 @@ workflow run_wf {
main:
output_ch = input_ch
| map { id, state ->
def quant_results = state.quant_type == 'kallisto' ? state.kallisto_quant_results : state.salmon_quant_results
[id, state + [quant_results: quant_results]]
}
| tx2gene.run (
fromState: [
"quant_results": "quant_results",
"gtf_extra_attributes": "gtf_extra_attributes",
"gtf": "gtf",
"gtf_group_features": "gtf_group_features",
"quant_type": "quant_type"
],
toState: [ "tx2gene_tsv": "tsv" ]
)
| map { id, state ->
def quant_results = state.quant_type == 'kallisto' ? state.kallisto_quant_results : state.salmon_quant_results
[id, state + [quant_results: quant_results]]
}
| tx2gene.run (
fromState: [
"quant_results": "quant_results",
"gtf_extra_attributes": "gtf_extra_attributes",
"gtf": "gtf",
"gtf_group_features": "gtf_group_features",
"quant_type": "quant_type"
],
toState: [ "tx2gene_tsv": "tsv" ]
)
| tximport.run (
fromState: [
"quant_results": "quant_results",
"tx2gene_tsv": "tx2gene_tsv",
"quant_type": "quant_type"
],
toState: [
"tpm_gene": "tpm_gene",
| tximport.run (
fromState: [
"quant_results": "quant_results",
"tx2gene_tsv": "tx2gene_tsv",
"quant_type": "quant_type"
],
toState: [
"tpm_gene": "tpm_gene",
"counts_gene": "counts_gene",
"counts_gene_length_scaled": "counts_gene_length_scaled",
"counts_gene_scaled": "counts_gene_scaled",
"tpm_transcript": "tpm_transcript",
"counts_transcript": "counts_transcript",
"length_gene": "length_gene",
"length_transcript": "length_transcript"
]
)
| summarizedexperiment.run (
fromState: [
"tpm_gene": "tpm_gene",
"counts_gene": "counts_gene",
"counts_gene_length_scaled": "counts_gene_length_scaled",
"counts_gene_scaled": "counts_gene_scaled",
"tpm_transcript": "tpm_transcript",
"counts_transcript": "counts_transcript",
"tx2gene_tsv": "tx2gene_tsv"
],
toState: [ "quant_merged_summarizedexperiment": "output" ]
)
| setState (
[ "tpm_gene": "tpm_gene",
"counts_gene": "counts_gene",
"counts_gene_length_scaled": "counts_gene_length_scaled",
"counts_gene_scaled": "counts_gene_scaled",
"tpm_transcript": "tpm_transcript",
"counts_transcript": "counts_transcript",
"length_gene": "length_gene",
"length_transcript": "length_transcript"
]
)
| summarizedexperiment.run (
fromState: [
"tpm_gene": "tpm_gene",
"counts_gene": "counts_gene",
"counts_gene_length_scaled": "counts_gene_length_scaled",
"counts_gene_scaled": "counts_gene_scaled",
"tpm_transcript": "tpm_transcript",
"counts_transcript": "counts_transcript",
"tx2gene_tsv": "tx2gene_tsv"
],
toState: [ "quant_merged_summarizedexperiment": "output" ]
)
| setState (
[ "tpm_gene": "tpm_gene",
"counts_gene": "counts_gene",
"counts_gene_length_scaled": "counts_gene_length_scaled",
"counts_gene_scaled": "counts_gene_scaled",
"tpm_transcript": "tpm_transcript",
"counts_transcript": "counts_transcript",
"quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment" ]
)
"quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment" ]
)
emit:
output_ch

4
target/executable/workflows/post_processing/.config.vsh.yaml
View File

@@ -486,8 +486,8 @@ build_info:
output: "target/executable/workflows/post_processing"
executable: "target/executable/workflows/post_processing/post_processing"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/picard_markduplicates"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"

284
target/executable/workflows/post_processing/post_processing
View File

@@ -1176,154 +1176,154 @@ workflow run_wf {
main:
output_ch = input_ch
| picard_markduplicates.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "genome_bam",
"fasta": "fasta",
"fai": "fai",
"extra_picard_args": "extra_picard_args"
],
toState: [
"processed_genome_bam": "output_bam",
"markduplicates_metrics": "metrics"
]
)
| samtools_sort.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [ "input": "processed_genome_bam" ],
toState: [ "processed_genome_bam": "output" ],
key: "genome_sorted_MarkDuplicates"
)
| samtools_index.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"input": "processed_genome_bam",
"csi": "bam_csi_index"
],
toState: [ "genome_bam_index": "output" ],
key: "genome_sorted_MarkDuplicates",
)
| samtools_stats.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"input": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_stats": "output" ],
key: "MarkDuplicates_stats"
)
| samtools_flagstat.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
| picard_markduplicates.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "genome_bam",
"fasta": "fasta",
"fai": "fai",
"extra_picard_args": "extra_picard_args"
],
toState: [
"processed_genome_bam": "output_bam",
"markduplicates_metrics": "metrics"
]
)
| samtools_sort.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [ "input": "processed_genome_bam" ],
toState: [ "processed_genome_bam": "output" ],
key: "genome_sorted_MarkDuplicates"
)
| samtools_index.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"input": "processed_genome_bam",
"csi": "bam_csi_index"
],
toState: [ "genome_bam_index": "output" ],
key: "genome_sorted_MarkDuplicates",
)
| samtools_stats.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"input": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_stats": "output" ],
key: "MarkDuplicates_stats"
)
| samtools_flagstat.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_flagstat": "output" ],
key: "MarkDuplicates_flagstat"
)
| samtools_idxstats.run(
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_flagstat": "output" ],
key: "MarkDuplicates_flagstat"
)
| samtools_idxstats.run(
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_idxstats": "output" ],
key: "MarkDuplicates_idxstats"
)
],
toState: [ "genome_bam_idxstats": "output" ],
key: "MarkDuplicates_idxstats"
)
| stringtie.run (
runIf: { id, state -> !state.skip_stringtie },
fromState: [
"strandedness": "strandedness",
"bam": "processed_genome_bam",
"annotation_gtf": "gtf",
"extra_stringtie_args": "extra_stringtie_args"
],
toState: [
"stringtie_transcript_gtf": "transcript_gtf",
"stringtie_coverage_gtf": "coverage_gtf",
"stringtie_abundance": "abundance",
"stringtie_ballgown": "ballgown"
]
)
| stringtie.run (
runIf: { id, state -> !state.skip_stringtie },
fromState: [
"strandedness": "strandedness",
"bam": "processed_genome_bam",
"annotation_gtf": "gtf",
"extra_stringtie_args": "extra_stringtie_args"
],
toState: [
"stringtie_transcript_gtf": "transcript_gtf",
"stringtie_coverage_gtf": "coverage_gtf",
"stringtie_abundance": "abundance",
"stringtie_ballgown": "ballgown"
]
)
// Genome-wide coverage with BEDTools
// 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: [
| 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"
]
)
| bedclip.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"input_bedgraph": "bedgraph_forward",
"sizes": "chrom_sizes"
],
toState: [ "bedgraph_forward": "output_bedgraph" ],
key: "bedclip_forward"
)
| bedgraphtobigwig.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"bedgraph": "bedgraph_forward",
"sizes": "chrom_sizes"
],
toState: [ "bigwig_forward": "bigwig" ],
key: "bedgraphtobigwig_forward"
)
| bedclip.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"input_bedgraph": "bedgraph_reverse",
"sizes": "chrom_sizes",
],
toState: [ "bedgraph_reverse": "output_bedgraph" ],
key: "bedclip_reverse"
)
| bedgraphtobigwig.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"bedgraph": "bedgraph_reverse",
"sizes": "chrom_sizes"
],
toState: [ "bigwig_reverse": "bigwig" ],
key: "bedgraphtobigwig_reverse"
)
| map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ]
}
| setState (
"processed_genome_bam": "processed_genome_bam",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"markduplicates_metrics": "markduplicates_metrics",
"stringtie_transcript_gtf": "stringtie_transcript_gtf",
"stringtie_coverage_gtf": "stringtie_coverage_gtf",
"stringtie_abundance": "stringtie_abundance",
"stringtie_ballgown": "stringtie_ballgown",
"bedgraph_forward": "bedgraph_forward",
"bedgraph_reverse": "bedgraph_reverse"
]
)
| bedclip.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"input_bedgraph": "bedgraph_forward",
"sizes": "chrom_sizes"
],
toState: [ "bedgraph_forward": "output_bedgraph" ],
key: "bedclip_forward"
)
| bedgraphtobigwig.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"bedgraph": "bedgraph_forward",
"sizes": "chrom_sizes"
],
toState: [ "bigwig_forward": "bigwig" ],
key: "bedgraphtobigwig_forward"
)
| bedclip.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"input_bedgraph": "bedgraph_reverse",
"sizes": "chrom_sizes",
],
toState: [ "bedgraph_reverse": "output_bedgraph" ],
key: "bedclip_reverse"
)
| bedgraphtobigwig.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"bedgraph": "bedgraph_reverse",
"sizes": "chrom_sizes"
],
toState: [ "bigwig_reverse": "bigwig" ],
key: "bedgraphtobigwig_reverse"
)
| map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ]
}
| setState (
"processed_genome_bam": "processed_genome_bam",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"markduplicates_metrics": "markduplicates_metrics",
"stringtie_transcript_gtf": "stringtie_transcript_gtf",
"stringtie_coverage_gtf": "stringtie_coverage_gtf",
"stringtie_abundance": "stringtie_abundance",
"stringtie_ballgown": "stringtie_ballgown",
"bedgraph_forward": "bedgraph_forward",
"bedgraph_reverse": "bedgraph_reverse",
"bigwig_forward": "bigwig_forward",
"bigwig_reverse": "bigwig_reverse"
)
"bedgraph_reverse": "bedgraph_reverse",
"bigwig_forward": "bigwig_forward",
"bigwig_reverse": "bigwig_reverse"
)
emit:
output_ch

4
target/executable/workflows/pre_processing/.config.vsh.yaml
View File

@@ -673,8 +673,8 @@ build_info:
output: "target/executable/workflows/pre_processing"
executable: "target/executable/workflows/pre_processing/pre_processing"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/fastqc"
- "target/nextflow/umitools/umitools_extract"

450
target/executable/workflows/pre_processing/pre_processing
View File

@@ -1540,238 +1540,238 @@ workflow run_wf {
main:
output_ch = input_ch
| map { id, state ->
def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
def paired = input.size() == 2
[ 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"
]
)
// Extract UMIs from fastq files and discard read 1 or read 2 if required
| umitools_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 ]
},
toState: [
"fastq_1": "fastq_1",
"fastq_2": "fastq_2"
]
)
// Discard read if required
| map { id, state ->
def paired = state.paired
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)
paired = false
| map { id, state ->
def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
def paired = input.size() == 2
[ id, state + [paired: paired, input: input] ]
}
[ id, state + [paired: paired, fastq_2: fastq_2] ]
}
// Trim reads using Trim galore!
| trimgalore.run (
runIf: { id, state -> !state.skip_trimming && state.trimmer == "trimgalore" },
fromState: { id, state ->
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 ]
},
toState: [
"fastq_1": "trimmed_r1",
"fastq_2": "trimmed_r2",
"trim_log_1": "trimming_report_r1",
"trim_log_2": "trimming_report_r2",
"trim_zip_1": "trimmed_fastqc_zip_1",
"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"
],
toState: [
"fastq_1": "out1",
"fastq_2": "out2",
"failed_trim": "failed_out",
"failed_trim_unpaired1": "unpaired1",
"failed_trim_unpaired2": "unpaired2",
"trim_json": "json",
"trim_html": "html",
"trim_merged_out": "merged_out"
]
)
// Perform FASTQC on reads trimmed using fastp
| 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"
],
key: "fastqc_trimming"
)
// Filter out contaminant RNA
| bbmap_bbsplit.run (
runIf: { id, state -> !state.skip_bbsplit },
fromState: { id, state ->
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
[ paired: state.paired,
input: input,
built_bbsplit_index: state.bbsplit_index ]
},
args: ["only_build_index": false],
toState: [
"fastq_1": "fastq_1",
"fastq_2": "fastq_2"
]
)
// Sort reads by rRNA and non-rRNA
| sortmerna.run (
runIf: { id, state -> state.remove_ribo_rna },
fromState: { id, state ->
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,
input: input,
ribo_database_manifest: refs ]
},
toState: [
"fastq_1": "fastq_1",
"fastq_2": "fastq_2",
"sortmerna_log": "sortmerna_log"
]
)
// 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
// 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"
]
},
toState: [
"subsampled_fastq_1": "output_1",
"subsampled_fastq_2": "output_2"
]
)
)
// Infer lib-type for salmon quant
| map { id, state ->
def lib_type = (state.paired) ?
(
(state.strandedness == "forward") ?
"ISF" :
(
(state.strandedness == "reverse") ? "ISR" : "IU"
)
)
: (
(state.strandedness == "forward") ?
"SF" :
(
(state.strandedness == "reverse") ? "SR" : "U"
)
)
[ id, state + [lib_type: lib_type] ]
}
| salmon_quant.run (
runIf: { id, state -> state.strandedness == 'auto' },
fromState: { id, state ->
def unmated_reads = !state.paired ? state.subsampled_fastq_1 : null
def mates1 = state.paired ? state.subsampled_fastq_1 : null
def mates2 = state.paired ? state.subsampled_fastq_2 : null
[ unmated_reads: unmated_reads,
mates1: mates1,
mates2: mates2,
gene_map: state.gtf,
index: state.salmon_index,
lib_type: state.lib_type ]
},
args: [ "skip_quant": true ],
toState: [ "salmon_quant_output": "output" ]
)
// Extract UMIs from fastq files and discard read 1 or read 2 if required
| umitools_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 ]
},
toState: [
"fastq_1": "fastq_1",
"fastq_2": "fastq_2"
]
)
// Discard read if required
| map { id, state ->
def paired = state.paired
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)
paired = false
}
[ id, state + [paired: paired, fastq_2: fastq_2] ]
}
| 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 ]
}
// Trim reads using Trim galore!
| trimgalore.run (
runIf: { id, state -> !state.skip_trimming && state.trimmer == "trimgalore" },
fromState: { id, state ->
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 ]
},
toState: [
"fastq_1": "trimmed_r1",
"fastq_2": "trimmed_r2",
"trim_log_1": "trimming_report_r1",
"trim_log_2": "trimming_report_r2",
"trim_zip_1": "trimmed_fastqc_zip_1",
"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]
)
| map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ]
}
// 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"
],
toState: [
"fastq_1": "out1",
"fastq_2": "out2",
"failed_trim": "failed_out",
"failed_trim_unpaired1": "unpaired1",
"failed_trim_unpaired2": "unpaired2",
"trim_json": "json",
"trim_html": "html",
"trim_merged_out": "merged_out"
]
)
| setState (
"fastqc_html_1": "fastqc_html_1",
"fastqc_html_2": "fastqc_html_2",
"fastqc_zip_1": "fastqc_zip_1",
"fastqc_zip_2": "fastqc_zip_2",
"qc_output1": "fastq_1",
"qc_output2": "fastq_2",
"trim_log_1": "trim_log_1",
"trim_log_2": "trim_log_2",
"trim_zip_1": "trim_zip_1",
"trim_zip_2": "trim_zip_2",
"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",
"salmon_quant_output": "salmon_quant_output"
)
// Perform FASTQC on reads trimmed using fastp
| 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"
],
key: "fastqc_trimming"
)
// Filter out contaminant RNA
| bbmap_bbsplit.run (
runIf: { id, state -> !state.skip_bbsplit },
fromState: { id, state ->
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
[ paired: state.paired,
input: input,
built_bbsplit_index: state.bbsplit_index ]
},
args: ["only_build_index": false],
toState: [
"fastq_1": "fastq_1",
"fastq_2": "fastq_2"
]
)
// Sort reads by rRNA and non-rRNA
| sortmerna.run (
runIf: { id, state -> state.remove_ribo_rna },
fromState: { id, state ->
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,
input: input,
ribo_database_manifest: refs ]
},
toState: [
"fastq_1": "fastq_1",
"fastq_2": "fastq_2",
"sortmerna_log": "sortmerna_log"
]
)
// 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
]
},
toState: [
"subsampled_fastq_1": "output_1",
"subsampled_fastq_2": "output_2"
]
)
// Infer lib-type for salmon quant
| map { id, state ->
def lib_type = (state.paired) ?
(
(state.strandedness == "forward") ?
"ISF" :
(
(state.strandedness == "reverse") ? "ISR" : "IU"
)
)
: (
(state.strandedness == "forward") ?
"SF" :
(
(state.strandedness == "reverse") ? "SR" : "U"
)
)
[ id, state + [lib_type: lib_type] ]
}
| salmon_quant.run (
runIf: { id, state -> state.strandedness == 'auto' },
fromState: { id, state ->
def unmated_reads = !state.paired ? state.subsampled_fastq_1 : null
def mates1 = state.paired ? state.subsampled_fastq_1 : null
def mates2 = state.paired ? state.subsampled_fastq_2 : null
[ unmated_reads: unmated_reads,
mates1: mates1,
mates2: mates2,
gene_map: state.gtf,
index: state.salmon_index,
lib_type: state.lib_type ]
},
args: [ "skip_quant": true ],
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.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ]
}
| setState (
"fastqc_html_1": "fastqc_html_1",
"fastqc_html_2": "fastqc_html_2",
"fastqc_zip_1": "fastqc_zip_1",
"fastqc_zip_2": "fastqc_zip_2",
"qc_output1": "fastq_1",
"qc_output2": "fastq_2",
"trim_log_1": "trim_log_1",
"trim_log_2": "trim_log_2",
"trim_zip_1": "trim_zip_1",
"trim_zip_2": "trim_zip_2",
"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",
"salmon_quant_output": "salmon_quant_output"
)
emit:
output_ch

4
target/executable/workflows/prepare_genome/.config.vsh.yaml
View File

@@ -509,8 +509,8 @@ build_info:
output: "target/executable/workflows/prepare_genome"
executable: "target/executable/workflows/prepare_genome/prepare_genome"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/gunzip"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread"

504
target/executable/workflows/prepare_genome/prepare_genome
View File

@@ -1176,278 +1176,280 @@ workflow run_wf {
main:
output_ch = input_ch
// Uncompress fasta
| gunzip.run (
fromState: [ "input": "fasta" ],
toState: [ "fasta": "output" ],
key: "gunzip_fasta",
args: [ output: "reference_genome.fasta" ]
)
// Uncompress fasta
| gunzip.run (
fromState: [ "input": "fasta" ],
toState: [ "fasta": "output" ],
key: "gunzip_fasta",
args: [ output: "reference_genome.fasta" ]
)
// uncompress gtf
| gunzip.run (
runIf: {id, state -> state.gtf},
fromState: [ "input": "gtf" ],
toState: [ "gtf": "output" ],
key: "gunzip_gtf",
args: [output: "gene_annotation.gtf"]
)
// uncompress gtf
| gunzip.run (
runIf: {id, state -> state.gtf},
fromState: [ "input": "gtf" ],
toState: [ "gtf": "output" ],
key: "gunzip_gtf",
args: [output: "gene_annotation.gtf"]
)
// uncompress gff
| gunzip.run (
runIf: {id, state -> !state.gtf && state.gff},
fromState: [ "input": "gff" ],
toState: [ "gff": "output" ],
key: "gunzip_gff",
args: [output: "gene_annotation.gff"]
)
// uncompress gff
| gunzip.run (
runIf: {id, state -> !state.gtf && state.gff},
fromState: [ "input": "gff" ],
toState: [ "gff": "output" ],
key: "gunzip_gff",
args: [output: "gene_annotation.gff"]
)
// gff to gtf
| gffread.run (
runIf: {id, state -> !state.gtf && state.gff},
fromState: [
"input": "gff",
"genome": "fasta"
],
toState: [ "gtf": "outfile" ],
args: [
outfile: "gene_annotation.gtf",
gtf_output: true
]
)
// gff to gtf
| gffread.run (
runIf: {id, state -> !state.gtf && state.gff},
fromState: [
"input": "gff",
"genome": "fasta"
],
toState: [ "gtf": "outfile" ],
args: [
outfile: "gene_annotation.gtf",
gtf_output: true,
keep_attrs: true,
keep_exon_attrs: true
]
)
| gtf_filter.run(
runIf: {id, state -> state.gtf && state.filter_gtf},
fromState: [
"fasta": "fasta",
"gtf": "gtf"
],
toState: [ "gtf": "filtered_gtf" ],
args: [filtered_gtf: "gene_annotation.gtf"]
)
| gtf_filter.run(
runIf: {id, state -> state.gtf && state.filter_gtf},
fromState: [
"fasta": "fasta",
"gtf": "gtf"
],
toState: [ "gtf": "filtered_gtf" ],
args: [filtered_gtf: "gene_annotation.gtf"]
)
// uncompress additional fasta
| gunzip.run (
runIf: {id, state -> state.additional_fasta},
fromState: [ "input": "additional_fasta" ],
toState: [ "additional_fasta": "output" ],
key: "gunzip_additional_fasta",
args: [output: "additional.fasta"]
)
// uncompress additional fasta
| gunzip.run (
runIf: {id, state -> state.additional_fasta},
fromState: [ "input": "additional_fasta" ],
toState: [ "additional_fasta": "output" ],
key: "gunzip_additional_fasta",
args: [output: "additional.fasta"]
)
// concatenate additional fasta
| cat_additional_fasta.run (
runIf: {id, state -> state.additional_fasta},
fromState: [
"fasta": "fasta",
"gtf": "gtf",
"additional_fasta": "additional_fasta",
"biotype": "biotype"
],
toState: [
"fasta": "fasta_output",
"gtf": "gtf_output"
],
args: [
fasta_output: "genome_additional.fasta",
gtf_output: "genome_additional.gtf"
]
)
// concatenate additional fasta
| cat_additional_fasta.run (
runIf: {id, state -> state.additional_fasta},
fromState: [
"fasta": "fasta",
"gtf": "gtf",
"additional_fasta": "additional_fasta",
"biotype": "biotype"
],
toState: [
"fasta": "fasta_output",
"gtf": "gtf_output"
],
args: [
fasta_output: "genome_additional.fasta",
gtf_output: "genome_additional.gtf"
]
)
// uncompress bed file
| gunzip.run (
runIf: {id, state -> state.gene_bed},
fromState: [ "input": "gene_bed" ],
toState: [ "gene_bed": "output" ],
key: "gunzip_gene_bed",
args: [output: "genome_additional.bed"]
)
// uncompress bed file
| gunzip.run (
runIf: {id, state -> state.gene_bed},
fromState: [ "input": "gene_bed" ],
toState: [ "gene_bed": "output" ],
key: "gunzip_gene_bed",
args: [output: "genome_additional.bed"]
)
// gtf to bed
| gtf2bed.run (
runIf: { id, state -> !state.gene_bed},
fromState: [ "gtf": "gtf" ],
toState: [ "gene_bed": "bed_output" ],
args: [bed_output: "genome_additional.bed"]
)
// gtf to bed
| gtf2bed.run (
runIf: { id, state -> !state.gene_bed},
fromState: [ "gtf": "gtf" ],
toState: [ "gene_bed": "bed_output" ],
args: [bed_output: "genome_additional.bed"]
)
// uncompress transcript fasta
| gunzip.run (
runIf: {id, state -> state.transcript_fasta},
fromState: [ "input": "transcript_fasta" ],
toState: [ "transcript_fasta": "output" ],
key: "transcript_fasta",
args: [output: "transcriptome.fasta"]
)
// uncompress transcript fasta
| gunzip.run (
runIf: {id, state -> state.transcript_fasta},
fromState: [ "input": "transcript_fasta" ],
toState: [ "transcript_fasta": "output" ],
key: "transcript_fasta",
args: [output: "transcriptome.fasta"]
)
// preprocess transcripts fasta if gtf is in gencode format
| preprocess_transcripts_fasta.run (
runIf: {id, state -> state.transcript_fasta && state.gencode},
fromState: [ "transcript_fasta": "transcript_fasta" ],
toState: [ "transcript_fasta": "output" ],
args: [output: "transcriptome.fasta"]
)
// preprocess transcripts fasta if gtf is in gencode format
| preprocess_transcripts_fasta.run (
runIf: {id, state -> state.transcript_fasta && state.gencode},
fromState: [ "transcript_fasta": "transcript_fasta" ],
toState: [ "transcript_fasta": "output" ],
args: [output: "transcriptome.fasta"]
)
// make transcript FASTA if not provided
| rsem_prepare_reference.run (
runIf: {id, state -> !state.transcript_fasta},
fromState: [
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
toState: [ "make_transcript_fasta_output": "output" ],
key: "make_transcript_fasta",\\
args: [reference_name: "genome"]
)
| map { id, state ->
def transcript_fasta = (!state.transcript_fasta) ?
state.make_transcript_fasta_output.listFiles().find{it.name == "genome.transcripts.fa"} :
state.transcript_fasta
[ id, state + [transcript_fasta: transcript_fasta] ]
}
// make transcript FASTA if not provided
| rsem_prepare_reference.run (
runIf: {id, state -> !state.transcript_fasta},
fromState: [
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
toState: [ "make_transcript_fasta_output": "output" ],
key: "make_transcript_fasta",
args: [reference_name: "genome"]
)
| map { id, state ->
def transcript_fasta = (!state.transcript_fasta) ?
state.make_transcript_fasta_output.listFiles().find{it.name == "genome.transcripts.fa"} :
state.transcript_fasta
[ 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"]
)
// 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"
)
// Uncompress STAR index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.star_index},
fromState: [ "input": "star_index" ],
toState: [ "star_index": "output" ],
key: "untar_star_index",
args: [output: "STAR_index"]
)
// TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode
| star_genome_generate.run (
runIf: {id, state -> !state.star_index && !state.skip_alignment},
fromState: [
"genome_fasta_files": "fasta",
"sjdb_gtf_file": "gtf",
"sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon"
],
toState: [ "star_index": "index" ],
key: "generate_star_index",
args: [index: "STAR_index"]
)
// Uncompress STAR index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.star_index},
fromState: [ "input": "star_index" ],
toState: [ "star_index": "output" ],
key: "untar_star_index",
args: [output: "STAR_index"]
)
// TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode
| star_genome_generate.run (
runIf: {id, state -> !state.star_index && !state.skip_alignment},
fromState: [
"genome_fasta_files": "fasta",
"sjdb_gtf_file": "gtf",
"sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon"
],
toState: [ "star_index": "index" ],
key: "generate_star_index",
args: [index: "STAR_index"]
)
// Uncompress RSEM index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.rsem_index},
fromState: [ "input": "rsem_index" ],
toState: [ "rsem_index": "output" ],
key: "untar_rsem_index",
args: [output: "RSEM_index"]
)
// Uncompress RSEM index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.rsem_index},
fromState: [ "input": "rsem_index" ],
toState: [ "rsem_index": "output" ],
key: "untar_rsem_index",
args: [output: "RSEM_index"]
)
| rsem_prepare_reference.run (
runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'},
fromState: [
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
toState: [ "rsem_index": "output" ],
key: "generate_rsem_index",
args: [reference_name: "genome"]
)
// TODO: Uncompress HISAT2 index or generate from scratch if required
| rsem_prepare_reference.run (
runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'},
fromState: [
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
toState: [ "rsem_index": "output" ],
key: "generate_rsem_index",
args: [reference_name: "genome"]
)
// TODO: Uncompress HISAT2 index or generate from scratch if required
// Uncompress Salmon index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.salmon_index},
fromState: [ "input": "salmon_index" ],
toState: [ "salmon_index": "output" ],
key: "untar_salmon_index",
args: [output: "Salmon_index"]
)
// Uncompress Salmon index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.salmon_index},
fromState: [ "input": "salmon_index" ],
toState: [ "salmon_index": "output" ],
key: "untar_salmon_index",
args: [output: "Salmon_index"]
)
| salmon_index.run (
runIf: {id, state -> (state.aligner == 'star_salmon' || state.pseudo_aligner == "salmon") && !state.salmon_index},
fromState: [
"genome": "fasta",
"transcripts": "transcript_fasta",
"kmer_len": "pseudo_aligner_kmer_size",
"gencode": "gencode"
],
toState: [ "salmon_index": "index" ],
key: "generate_salmon_index",
args: [index: "Salmon_index"]
)
| salmon_index.run (
runIf: {id, state -> (state.aligner == 'star_salmon' || state.pseudo_aligner == "salmon") && !state.salmon_index},
fromState: [
"genome": "fasta",
"transcripts": "transcript_fasta",
"kmer_len": "pseudo_aligner_kmer_size",
"gencode": "gencode"
],
toState: [ "salmon_index": "index" ],
key: "generate_salmon_index",
args: [index: "Salmon_index"]
)
// Uncompress Kallisto index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.kallisto_index},
fromState: [ "input": "kallisto_index" ],
toState: [ "kallisto_index": "output" ],
key: "untar_kallisto_index",
args: [output: "Kallisto_index"]
)
// Uncompress Kallisto index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.kallisto_index},
fromState: [ "input": "kallisto_index" ],
toState: [ "kallisto_index": "output" ],
key: "untar_kallisto_index",
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: [
"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"]
)
| 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 (
"fasta_uncompressed": "fasta",
"gtf_uncompressed": "gtf",
"transcript_fasta_uncompressed": "transcript_fasta",
"gene_bed_uncompressed": "gene_bed",
"star_index_uncompressed": "star_index",
"salmon_index_uncompressed": "salmon_index",
"kallisto_index_uncompressed": "kallisto_index",
"bbsplit_index_uncompressed": "bbsplit_index",
"rsem_index_uncompressed": "rsem_index",
"chrom_sizes": "sizes",
"fai": "fai"
)
| setState (
"fasta_uncompressed": "fasta",
"gtf_uncompressed": "gtf",
"transcript_fasta_uncompressed": "transcript_fasta",
"gene_bed_uncompressed": "gene_bed",
"star_index_uncompressed": "star_index",
"salmon_index_uncompressed": "salmon_index",
"kallisto_index_uncompressed": "kallisto_index",
"bbsplit_index_uncompressed": "bbsplit_index",
"rsem_index_uncompressed": "rsem_index",
"chrom_sizes": "sizes",
"fai": "fai"
)
emit:
output_ch

4
target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml
View File

@@ -283,8 +283,8 @@ 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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
- "target/nextflow/kallisto/kallisto_quant"

151
target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant
View File

@@ -806,86 +806,87 @@ workflow run_wf {
main:
output_ch = input_ch
| map { id, state ->
def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
def paired = input.size() == 2
[ id, state + [ paired: paired, input: input ] ]
}
// Infer lib-type for salmon quant
| map { id, state ->
def lib_type = (state.paired) ?
(
(state.strandedness == "forward") ?
"ISF" :
(
(state.strandedness == "reverse") ? "ISR" : "IU"
)
)
: (
(state.strandedness == "forward") ?
"SF" :
(
(state.strandedness == "reverse") ? "SR" : "U"
)
)
[ id, state + [lib_type: lib_type] ]
}
// Count reads from BAM alignments using Salmon
| salmon_quant.run (
runIf: { id, state -> state.pseudo_aligner == 'salmon' },
fromState: { id, state ->
def unmated_reads = !state.paired ? state.fastq_1 : null
def mates1 = state.paired ? state.fastq_1 : null
def mates2 = state.paired ? state.fastq_2 : null
[ unmated_reads: unmated_reads,
mates1: mates1,
mates2: mates2,
gene_map: state.gtf,
index: state.salmon_index,
lib_type: state.lib_type ]
},
toState: [
"quant_out_dir": "output",
"salmon_quant_results_file": "quant_results"
]
)
| map { id, state ->
def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
def paired = input.size() == 2
[ id, state + [ paired: paired, input: input ] ]
}
| map { id, state ->
def mod_state = (state.pseudo_aligner == 'salmon') ? state + [pseudo_multiqc: state.quant_out_dir] : state
[ 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"
]
)
// Infer lib-type for salmon quant
| map { id, state ->
def lib_type = (state.paired) ?
(
(state.strandedness == "forward") ?
"ISF" :
(
(state.strandedness == "reverse") ? "ISR" : "IU"
)
)
: (
(state.strandedness == "forward") ?
"SF" :
(
(state.strandedness == "reverse") ? "SR" : "U"
)
)
[ id, state + [lib_type: lib_type] ]
}
// Count reads from BAM alignments using Salmon
| salmon_quant.run (
runIf: { id, state -> state.pseudo_aligner == 'salmon' },
fromState: { id, state ->
def unmated_reads = !state.paired ? state.fastq_1 : null
def mates1 = state.paired ? state.fastq_1 : null
def mates2 = state.paired ? state.fastq_2 : null
[ unmated_reads: unmated_reads,
mates1: mates1,
mates2: mates2,
gene_map: state.gtf,
index: state.salmon_index,
lib_type: state.lib_type ]
},
toState: [
"quant_out_dir": "output",
"salmon_quant_results_file": "quant_results"
]
)
| 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.pseudo_aligner == 'salmon') ? state + [pseudo_multiqc: state.quant_out_dir] : state
[ id, mod_state ]
}
| setState (
[ "pseudo_multiqc": "quant_results",
"quant_out_dir": "quant_out_dir",
"salmon_quant_results_file": "salmon_quant_results_file",
"kallisto_quant_results_file": "kallisto_quant_results_file" ]
)
| 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"
]
)
| map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ]
}
| setState (
[ "pseudo_multiqc": "quant_results",
"quant_out_dir": "quant_out_dir",
"salmon_quant_results_file": "salmon_quant_results_file",
"kallisto_quant_results_file": "kallisto_quant_results_file" ]
)
emit:
output_ch

8
target/executable/workflows/quality_control/.config.vsh.yaml
View File

@@ -295,7 +295,7 @@ argument_groups:
description: "Specify the RSeQC modules to run_wf"
info: null
default:
- "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication"
- "bam_stat;inner_distance;infer_experiment;junction_annotation;junction_saturation;read_distribution;read_duplication"
required: false
choices:
- "bam_stat"
@@ -308,7 +308,7 @@ argument_groups:
- "tin"
direction: "input"
multiple: true
multiple_sep: ","
multiple_sep: ";"
- type: "integer"
name: "--sample_size"
description: "Numer of reads sampled from SAM/BAM file to infer experiment and\
@@ -1556,8 +1556,8 @@ build_info:
output: "target/executable/workflows/quality_control"
executable: "target/executable/workflows/quality_control/quality_control"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/rseqc/rseqc_bamstat"
- "target/nextflow/rseqc/rseqc_inferexperiment"

1412
target/executable/workflows/quality_control/quality_control
View File

File diff suppressed because it is too large Load Diff

38
target/executable/workflows/rnaseq/.config.vsh.yaml
View File

@@ -693,10 +693,10 @@ argument_groups:
multiple_sep: ";"
- type: "string"
name: "--rseqc_modules"
description: "Specify the RSeQC modules to run_wf"
description: "Specify the RSeQC modules to run_wf (comma-separated list)"
info: null
default:
- "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication"
- "bam_stat;inner_distance;infer_experiment;junction_annotation;junction_saturation;read_distribution;read_duplication"
required: false
choices:
- "bam_stat"
@@ -709,8 +709,8 @@ argument_groups:
- "tin"
direction: "input"
multiple: true
multiple_sep: ","
- name: "Multiqc paramenters"
multiple_sep: ";"
- name: "MultiQC paramenters"
arguments:
- type: "file"
name: "--multiqc_custom_config"
@@ -840,7 +840,7 @@ argument_groups:
description: "Path to output directory"
info: null
default:
- "fastq/$id.read_1.fastq"
- "fastq/$id.read_1.fastq.gz"
must_exist: false
create_parent: true
required: false
@@ -852,7 +852,7 @@ argument_groups:
description: "Path to output directory"
info: null
default:
- "fastq/$id.read_2.fastq"
- "fastq/$id.read_2.fastq.gz"
must_exist: false
create_parent: true
required: false
@@ -1865,6 +1865,17 @@ argument_groups:
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--deseq2_output_pseudo"
info: null
default:
- "deseq2_qc_pseudo"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--multiqc_report"
info: null
@@ -1940,6 +1951,17 @@ argument_groups:
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pseudo_tpm_gene"
info: null
default:
- "pseudo_alignment_quantification/gene_tpm.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pseudo_tpm_transcript"
info: null
@@ -2090,8 +2112,8 @@ build_info:
output: "target/executable/workflows/rnaseq"
executable: "target/executable/workflows/rnaseq/rnaseq"
viash_version: "0.9.0"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/workflows/prepare_genome"
- "target/nextflow/cat_fastq"

970
target/executable/workflows/rnaseq/rnaseq
View File

File diff suppressed because it is too large Load Diff