diff --git a/configs/conda.config b/configs/conda.config index 2e95f78..04d1fa5 100644 --- a/configs/conda.config +++ b/configs/conda.config @@ -3,6 +3,7 @@ process { withLabel: minimap2 { conda = "$baseDir/envs/minimap2.yaml" } withLabel: python3 { conda = "$baseDir/envs/python3.yaml" } withLabel: deseq2 { conda = "$baseDir/envs/deseq2.yaml" } + withLabel: webgestalt { conda = "$baseDir/envs/webgestalt.yaml" } withLabel: fastp { conda = "$baseDir/envs/fastp.yaml" } withLabel: fastqc { conda = "$baseDir/envs/fastqc.yaml" } withLabel: nanoplot { conda = "$baseDir/envs/nanoplot.yaml" } diff --git a/configs/container.config b/configs/container.config index c010a5d..33ab635 100644 --- a/configs/container.config +++ b/configs/container.config @@ -3,6 +3,7 @@ process { withLabel: minimap2 { container = "nanozoo/minimap2:2.22--b178b67" } withLabel: python3 { container = "nanozoo/python_rnaseq:3--23823db" } withLabel: deseq2 { container = "nanozoo/deseq2:1.34.0--c670fa0" } + withLabel: webgestalt { container = "nanozoo/webgestalt:0.4.6--5a8d95e" } withLabel: fastp { container = "nanozoo/fastp:0.23.1--9f2e255" } withLabel: fastqc { container = "nanozoo/fastqc:0.11.8--fbfa1d7" } withLabel: subread { container = "nanozoo/subread:2.0.1--713a8e7" } diff --git a/configs/local.config b/configs/local.config index 6d04308..59b5226 100644 --- a/configs/local.config +++ b/configs/local.config @@ -2,6 +2,7 @@ process { withLabel: hisat2 { cpus = params.cores } withLabel: minimap2 { cpus = params.cores } withLabel: deseq2 { cpus = params.cores } + withLabel: webgestalt { cpus = params.cores } withLabel: fastp { cpus = params.cores } withLabel: fastqc { cpus = 1 } withLabel: subread { cpus = params.cores } diff --git a/configs/nodes.config b/configs/nodes.config index 07c6b9d..1392480 100644 --- a/configs/nodes.config +++ b/configs/nodes.config @@ -11,4 +11,5 @@ process { withLabel: dammit { cpus = 42 ; memory = '42 GB' } withLabel: rattle { cpus = 32; memory = '32 GB' } withLabel: smallTask { cpus = 1; memory = '1 GB' } + withLabel: webgestalt { cpus = 1; memory = '4 GB' } } diff --git a/envs/deseq2.yaml b/envs/deseq2.yaml index f3de9de..b8e9cfd 100644 --- a/envs/deseq2.yaml +++ b/envs/deseq2.yaml @@ -22,7 +22,6 @@ dependencies: - r-openxlsx=4.2.5 - r-doparallel=1.0.17 - r-foreach=1.5.2 - - r-webgestaltr=0.4.4 - r-upsetr=1.4.0 - r-sessioninfo=1.2.2 - r-knitcitations=1.0.12 diff --git a/envs/webgestalt.yaml b/envs/webgestalt.yaml new file mode 100644 index 0000000..4a132e5 --- /dev/null +++ b/envs/webgestalt.yaml @@ -0,0 +1,9 @@ +name: webgestalt +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - r-base + - r-webgestaltr=0.4.6 + - zip==3.0 \ No newline at end of file diff --git a/modules/webgestalt.nf b/modules/webgestalt.nf index b590d1b..52353fe 100644 --- a/modules/webgestalt.nf +++ b/modules/webgestalt.nf @@ -1,5 +1,5 @@ process webgestalt { - label 'deseq2' + label 'webgestalt' tag "$comparison" publishDir "${params.output}/${params.deseq2_dir}/${comparison}/downstream_analysis", mode: 'copy', pattern: "WebGestalt" @@ -19,6 +19,8 @@ process webgestalt { script: comparison = resFold05.toString().split("deseq2_")[1].split("_filtered")[0]//findAll("[a-zA-Z]*_vs_[a-zA-Z]*")[0] """ + # set env var for zip command for zipping in webgestalt since sometimes its not set in conda envs somehow and crashes the report making + export R_ZIPCMD=\$(which zip) R CMD BATCH --no-save --no-restore '--args c(".") c("${resFold05}") c("${species}") c("${id_type}")' ${webgestalt_script} """ }