diff --git a/src/nf_modules/BWA/indexing.config b/src/nf_modules/BWA/indexing.config index acc8e53965a06dd94f2e7d99cad7af6297a24b5a..2936204f3dc8475073f98ae24c4dcdb70a6dfda9 100644 --- a/src/nf_modules/BWA/indexing.config +++ b/src/nf_modules/BWA/indexing.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: index_fasta { + withName: index_fasta { container = "bwa:0.7.17" } } } psmn { process{ - withname: index_fasta { + withName: index_fasta { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "BWA/0.7.17" executor = "sge" diff --git a/src/nf_modules/BWA/mapping_paired.config b/src/nf_modules/BWA/mapping_paired.config index 808e12a66c16ebe1dc3a417a0e1970cdb7719598..ce8f7f4582171b245b9a1162779007916f999122 100644 --- a/src/nf_modules/BWA/mapping_paired.config +++ b/src/nf_modules/BWA/mapping_paired.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: mapping_fastq { + withName: mapping_fastq { container = "bwa:0.7.17" } } } psmn { process{ - withname: mapping_fastq { + withName: mapping_fastq { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "BWA/0.7.17" executor = "sge" diff --git a/src/nf_modules/Bowtie/indexing.config b/src/nf_modules/Bowtie/indexing.config index a1b6addd32b7f2b1aaec792d11284879c9095e4c..954b245efedf9c30a32748e21c4368b3ac7cd733 100644 --- a/src/nf_modules/Bowtie/indexing.config +++ b/src/nf_modules/Bowtie/indexing.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: index_fasta { + withName: index_fasta { container = "bowtie:1.2.2" } } } psmn { process{ - withname: index_fasta { + withName: index_fasta { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "Bowtie/1.2.2" executor = "sge" diff --git a/src/nf_modules/Bowtie/mapping_paired.config b/src/nf_modules/Bowtie/mapping_paired.config index 9d661f3fe01b9169d447644d2a0508764e7edf61..5b3b9f95a39eaf871ed6d2dbd274a94cbfeb41f0 100644 --- a/src/nf_modules/Bowtie/mapping_paired.config +++ b/src/nf_modules/Bowtie/mapping_paired.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: mapping_fastq { + withName: mapping_fastq { container = "bowtie:1.2.2" } } } psmn { process{ - withname: mapping_fastq { + withName: mapping_fastq { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "Bowtie/1.2.2:SAMtools/1.7" executor = "sge" diff --git a/src/nf_modules/Bowtie/mapping_single.config b/src/nf_modules/Bowtie/mapping_single.config index 9d661f3fe01b9169d447644d2a0508764e7edf61..5b3b9f95a39eaf871ed6d2dbd274a94cbfeb41f0 100644 --- a/src/nf_modules/Bowtie/mapping_single.config +++ b/src/nf_modules/Bowtie/mapping_single.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: mapping_fastq { + withName: mapping_fastq { container = "bowtie:1.2.2" } } } psmn { process{ - withname: mapping_fastq { + withName: mapping_fastq { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "Bowtie/1.2.2:SAMtools/1.7" executor = "sge" diff --git a/src/nf_modules/Bowtie2/indexing.config b/src/nf_modules/Bowtie2/indexing.config index 82ebc902dd50c724072a774024d7f5e0eaa8a32c..434889bc922c66338e8459cb6990fb43e0d04ea1 100644 --- a/src/nf_modules/Bowtie2/indexing.config +++ b/src/nf_modules/Bowtie2/indexing.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: mapping_fastq { + withName: mapping_fastq { container = "bowtie2:2.3.4.1" } } } psmn { process{ - withname: mapping_fastq { + withName: mapping_fastq { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "Bowtie2/2.3.4.1" executor = "sge" diff --git a/src/nf_modules/Bowtie2/mapping_paired.config b/src/nf_modules/Bowtie2/mapping_paired.config index 8fe161a0f7eee81dd2ec8e19926078ca52c161f0..30150ff97c6cbc333746b0a86d08c8da8db34c13 100644 --- a/src/nf_modules/Bowtie2/mapping_paired.config +++ b/src/nf_modules/Bowtie2/mapping_paired.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: mapping_fastq { + withName: mapping_fastq { container = "bowtie2:2.3.4.1" } } } psmn { process{ - withname: mapping_fastq { + withName: mapping_fastq { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "Bowtie2/2.3.4.1:SAMtools/1.7" executor = "sge" diff --git a/src/nf_modules/Bowtie2/mapping_single.config b/src/nf_modules/Bowtie2/mapping_single.config index 8fe161a0f7eee81dd2ec8e19926078ca52c161f0..30150ff97c6cbc333746b0a86d08c8da8db34c13 100644 --- a/src/nf_modules/Bowtie2/mapping_single.config +++ b/src/nf_modules/Bowtie2/mapping_single.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: mapping_fastq { + withName: mapping_fastq { container = "bowtie2:2.3.4.1" } } } psmn { process{ - withname: mapping_fastq { + withName: mapping_fastq { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "Bowtie2/2.3.4.1:SAMtools/1.7" executor = "sge" diff --git a/src/nf_modules/FastQC/fastqc_paired.config b/src/nf_modules/FastQC/fastqc_paired.config index b16c5d07c5647284cf8f36184f7f527e0e0af94b..9fda3d13c30902d0ad7d42f951a3095576efaec9 100644 --- a/src/nf_modules/FastQC/fastqc_paired.config +++ b/src/nf_modules/FastQC/fastqc_paired.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: fastqc_fastq { + withName: fastqc_fastq { container = "fastqc:0.11.5" } } } psmn { process{ - withname: fastqc_fastq { + withName: fastqc_fastq { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "FastQC/0.11.5" executor = "sge" diff --git a/src/nf_modules/FastQC/fastqc_single.config b/src/nf_modules/FastQC/fastqc_single.config index b16c5d07c5647284cf8f36184f7f527e0e0af94b..9fda3d13c30902d0ad7d42f951a3095576efaec9 100644 --- a/src/nf_modules/FastQC/fastqc_single.config +++ b/src/nf_modules/FastQC/fastqc_single.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: fastqc_fastq { + withName: fastqc_fastq { container = "fastqc:0.11.5" } } } psmn { process{ - withname: fastqc_fastq { + withName: fastqc_fastq { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "FastQC/0.11.5" executor = "sge" diff --git a/src/nf_modules/HTSeq/htseq.config b/src/nf_modules/HTSeq/htseq.config index 95919f56151da4bda93cb7ec5138a38dc6c34c27..87368e139794cfdbb8c577f657e2ecbee0871479 100644 --- a/src/nf_modules/HTSeq/htseq.config +++ b/src/nf_modules/HTSeq/htseq.config @@ -3,17 +3,17 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: sort_bam { + withName: sort_bam { container = "samtools:1.7" } - withname: counting { + withName: counting { container = "htseq:0.8.0" } } } psmn { process{ - withname: sort_bam { + withName: sort_bam { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "SAMtools/1.7" executor = "sge" @@ -22,7 +22,7 @@ profiles { time = "12h" queue = 'monointeldeb128' } - withname: trimming { + withName: trimming { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "HTSeq/0.8.0" executor = "sge" diff --git a/src/nf_modules/MUSIC/peak_calling_single.config b/src/nf_modules/MUSIC/peak_calling_single.config index f8ad13e20a1ff1b58914dc982b636fcde9825922..2d7145ae1ff375606278d855a02587f069ff6d13 100644 --- a/src/nf_modules/MUSIC/peak_calling_single.config +++ b/src/nf_modules/MUSIC/peak_calling_single.config @@ -3,20 +3,20 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: compute_mappability { + withName: compute_mappability { container = "music:6613c53" } - withname: music_preprocessing { + withName: music_preprocessing { container = "music:6613c53" } - withname: music_computation { + withName: music_computation { container = "music:6613c53" } } } psmn { process{ - withname: compute_mappability { + withName: compute_mappability { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "MUSIC/6613c53" executor = "sge" @@ -25,7 +25,7 @@ profiles { time = "12h" queue = 'monointeldeb128' } - withname: music_preprocessing { + withName: music_preprocessing { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "MUSIC/6613c53" executor = "sge" @@ -34,7 +34,7 @@ profiles { time = "12h" queue = 'monointeldeb128' } - withname: music_computation { + withName: music_computation { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "MUSIC/6613c53" executor = "sge" diff --git a/src/nf_modules/MultiQC/multiqc_paired.config b/src/nf_modules/MultiQC/multiqc_paired.config index d986c1f04e9da521be57b31ece221375cb649db7..592b63c23d50b1e541e7bf981f5e41e2e71ebd03 100644 --- a/src/nf_modules/MultiQC/multiqc_paired.config +++ b/src/nf_modules/MultiQC/multiqc_paired.config @@ -4,17 +4,17 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: fastqc_fastq { + withName: fastqc_fastq { container = "fastqc:0.11.5" } - withname: multiqc { + withName: multiqc { container = "multiqc:1.0" } } } psmn { process{ - withname: fastqc_fastq { + withName: fastqc_fastq { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "FastQC/0.11.5" executor = "sge" @@ -25,7 +25,7 @@ profiles { pollInterval = '60sec' queue = 'monointeldeb128' } - withname: multiqc { + withName: multiqc { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "MultiQC/1.0" executor = "sge" diff --git a/src/nf_modules/MultiQC/multiqc_single.config b/src/nf_modules/MultiQC/multiqc_single.config index a6a2948abb303672c4f76d895cf0e383723e745c..7f6bf3d94940eece66b6febd9f2313b43e4236d0 100644 --- a/src/nf_modules/MultiQC/multiqc_single.config +++ b/src/nf_modules/MultiQC/multiqc_single.config @@ -3,17 +3,17 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: fastqc_fastq { + withName: fastqc_fastq { container = "fastqc:0.11.5" } - withname: multiqc { + withName: multiqc { container = "multiqc:1.0" } } } psmn { process{ - withname: fastqc_fastq { + withName: fastqc_fastq { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "FastQC/0.11.5" executor = "sge" @@ -24,7 +24,7 @@ profiles { pollInterval = '60sec' queue = 'monointeldeb128' } - withname: multiqc { + withName: multiqc { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "MultiQC/1.0" executor = "sge" diff --git a/src/nf_modules/RSEM/indexing.config b/src/nf_modules/RSEM/indexing.config index d6d0a9086f0e7da710efa8eddc4069bed07bd9f2..c0d3287e2e2de4e96ab8d188511bf44bb0c538cb 100644 --- a/src/nf_modules/RSEM/indexing.config +++ b/src/nf_modules/RSEM/indexing.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: index_fasta { + withName: index_fasta { container = "rsem:1.3.0" } } } psmn { process{ - withname: index_fasta { + withName: index_fasta { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "RSEM/1.3.0:SAMtools/1.7" executor = "sge" diff --git a/src/nf_modules/RSEM/quantification_paired.config b/src/nf_modules/RSEM/quantification_paired.config index 0801e388291866630253a09a3eb4519feec87498..46ff1549641ae6bca4429b0c4f880c01d3479039 100644 --- a/src/nf_modules/RSEM/quantification_paired.config +++ b/src/nf_modules/RSEM/quantification_paired.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: mapping_fastq { + withName: mapping_fastq { container = "rsem:1.3.0" } } } psmn { process{ - withname: mapping_fastq { + withName: mapping_fastq { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "RSEM/1.3.0:SAMtools/1.7" executor = "sge" diff --git a/src/nf_modules/RSEM/quantification_single.config b/src/nf_modules/RSEM/quantification_single.config index 0801e388291866630253a09a3eb4519feec87498..46ff1549641ae6bca4429b0c4f880c01d3479039 100644 --- a/src/nf_modules/RSEM/quantification_single.config +++ b/src/nf_modules/RSEM/quantification_single.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: mapping_fastq { + withName: mapping_fastq { container = "rsem:1.3.0" } } } psmn { process{ - withname: mapping_fastq { + withName: mapping_fastq { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "RSEM/1.3.0:SAMtools/1.7" executor = "sge" diff --git a/src/nf_modules/SAMtools/filter_bams.config b/src/nf_modules/SAMtools/filter_bams.config index a000c5cdbf7bc776fa33ed3e40396eb1503a9c0d..ef3aa49103b3e1181ed5164974f089c2467bf05f 100644 --- a/src/nf_modules/SAMtools/filter_bams.config +++ b/src/nf_modules/SAMtools/filter_bams.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: filter_bam { + withName: filter_bam { container = "samtools:1.7" } } } psmn { process{ - withname: filter_bam { + withName: filter_bam { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "SAMtools/1.7" executor = "sge" diff --git a/src/nf_modules/SAMtools/index_bams.config b/src/nf_modules/SAMtools/index_bams.config index c44c2e73817c91ac8555f35540c4c200a0251ffc..135b6b3a98579e4d7aca56c75699be13121cb93b 100644 --- a/src/nf_modules/SAMtools/index_bams.config +++ b/src/nf_modules/SAMtools/index_bams.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: index_bam { + withName: index_bam { container = "samtools:1.7" } } } psmn { process{ - withname: index_bam { + withName: index_bam { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "SAMtools/1.7" executor = "sge" diff --git a/src/nf_modules/SAMtools/sort_bams.config b/src/nf_modules/SAMtools/sort_bams.config index c0e08d020404d8b850974c71a53d148eec71bdd6..1c1bdca5a5f1f60e786564e9ae40f333cb11f0c9 100644 --- a/src/nf_modules/SAMtools/sort_bams.config +++ b/src/nf_modules/SAMtools/sort_bams.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: sort_bam { + withName: sort_bam { container = "samtools:1.7" } } } psmn { process{ - withname: sort_bam { + withName: sort_bam { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "SAMtools/1.7" executor = "sge" diff --git a/src/nf_modules/SAMtools/split_bams.config b/src/nf_modules/SAMtools/split_bams.config index 3ef8321eee08c38806aae6e9401f45333efb02b6..15880281e363b4de61a362ffe6bc67bba704242f 100644 --- a/src/nf_modules/SAMtools/split_bams.config +++ b/src/nf_modules/SAMtools/split_bams.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: split_bam { + withName: split_bam { container = "samtools:1.7" } } } psmn { process{ - withname: split_bam { + withName: split_bam { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "SAMtools/1.7" executor = "sge" diff --git a/src/nf_modules/SRAtoolkit/fastqdump.config b/src/nf_modules/SRAtoolkit/fastqdump.config index edd7856acd5e28209b43efb295eca627d61f4a8a..67676b9ad635f80b8973db656ba43de1635bd39e 100644 --- a/src/nf_modules/SRAtoolkit/fastqdump.config +++ b/src/nf_modules/SRAtoolkit/fastqdump.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: fastq_dump { + withName: fastq_dump { container = "sratoolkit:2.8.2" } } } psmn { process{ - withname: fastq_dump { + withName: fastq_dump { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "SRAtoolkit/2.8.2" executor = "sge" diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config index 6bbae437064053b81f104ba7c3a48abf9b343db2..22fc18de5046b1bdd0f3626b0dad76715c98b4b4 100644 --- a/src/nf_modules/sambamba/index_bams.config +++ b/src/nf_modules/sambamba/index_bams.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: index_bam { + withName: index_bam { container = "sambamba:0.6.7" } } } psmn { process{ - withname: index_bam { + withName: index_bam { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "sambamba/0.6.7" executor = "sge" diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config index c60ee44e65201802676a351cee8f776ffda59194..9dd63fcaf6aee0afdc36daf4c2750a88c27a26f5 100644 --- a/src/nf_modules/sambamba/sort_bams.config +++ b/src/nf_modules/sambamba/sort_bams.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: sort_bam { + withName: sort_bam { container = "sambamba:0.6.7" } } } psmn { process{ - withname: sort_bam { + withName: sort_bam { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "sambamba/0.6.7" executor = "sge" diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config index 51afa4faef749ff287e11bff0869ab321e6cb858..3b9acd7257269b8f009e1f277cbc68645afa7efe 100644 --- a/src/nf_modules/sambamba/split_bams.config +++ b/src/nf_modules/sambamba/split_bams.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: split_bam { + withName: split_bam { container = "sambamba:0.6.7" } } } psmn { process{ - withname: split_bam { + withName: split_bam { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "sambamba/0.6.7" executor = "sge" diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config index 6aeaec5fb5cfa2d2eb9c4467bc82b32fdb4bb93f..42e3757cc206d52cc96a4dcdab48f5c3f41fa1c3 100644 --- a/src/nf_modules/samblaster/dedup_sams.config +++ b/src/nf_modules/samblaster/dedup_sams.config @@ -3,14 +3,14 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - withname: dedup_sam { + withName: dedup_sam { container = "samblaster:0.1.24" } } } psmn { process{ - withname: dedup_sam { + withName: dedup_sam { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "samblaster/0.1.24" executor = "sge"