diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config index a8a0c0052337d856235a9ce86ae8398d2baf48e3..d7537dbd2e9a4eb56159362b6fa51c0210fb1948 100755 --- a/workflow/conf/biohpc.config +++ b/workflow/conf/biohpc.config @@ -2,13 +2,13 @@ process { executor = 'slurm' queue = 'super' clusterOptions = '--hold' + container = 'docker://bicf/bicfbase:1.3' withLabel:checkDesignFile { container = 'docker://bicf/python3:1.2' executor = 'local' } withLabel:untarBCL { - container = 'docker://bicf/bicfbase:1.3' queue = 'super' } withLabel:mkfastq { @@ -16,7 +16,6 @@ process { queue = '128GB,256GB,256GBv1,384GB' } withLabel:countDesign { - container = 'docker://bicf/bicfbase:1.3' executor = 'local' } withLabel:fastqc { diff --git a/workflow/conf/biohpc_local.config b/workflow/conf/biohpc_local.config index 53528117be7e55df9c3c53a6f6e448e75564cf1a..f1e2a31b1e68e3839172fc2946841d123bfb747e 100644 --- a/workflow/conf/biohpc_local.config +++ b/workflow/conf/biohpc_local.config @@ -1,17 +1,16 @@ process { executor = 'local' + container = 'docker://bicf/bicfbase:1.3' withLabel:checkDesignFile { container = 'docker://bicf/python3:1.2' } withLabel:untarBCL { - container = 'docker://bicf/bicfbase:1.3' } withLabel:mkfastq { container = 'docker://bicf/cellranger3.1.0:1.0' } withLabel:countDesign { - container = 'docker://bicf/bicfbase:1.3' } withLabel:fastqc { module = ['fastqc/0.11.5', 'parallel'] diff --git a/workflow/nextflow.config b/workflow/nextflow.config index ee8637aac8db277be69dd29af4941ba44b80b13a..b8067535152fb1833b1fd1a49595491d945c5eed 100644 --- a/workflow/nextflow.config +++ b/workflow/nextflow.config @@ -30,14 +30,14 @@ report { } tower { - accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f' enabled = true + accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f' } manifest { - homePage = 'https://https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq' + homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq' description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.' mainScript = 'main.nf' version = 'v1.4.0_indev' - nextflowVersion = '>=19.09.0' + nextflowVersion = '>=0.31.0' } \ No newline at end of file