diff --git a/src/.update_config.sh b/src/.update_config.sh index 3e7c6a1e8f6a7b9c01b5d27bb8fc05cb14a4a633..c591051e470b6a6690978ed95a7c313b3c993c29 100644 --- a/src/.update_config.sh +++ b/src/.update_config.sh @@ -17,3 +17,9 @@ fd ".*config" -E "nf_modules" src/ -x perl -0777pe "s|\s*ccin2p3_conda {.*ccin2p # we update the psmn module to conda fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"\n\s*module = "(.*)/(.*)"|beforeScript = "source \$baseDir/.conda_psmn.sh"\n conda = "\$baseDir/.conda_envs/\L\1_\2"|mg' -i {} + +# we update the psmn queue to new cluster +fd ".*config" src/ -x perl -0777pe 's|E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F|CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D|mg' -i {} +fd ".*config" src/ -x perl -0777pe 's|monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128|monointeldeb128|mg' -i {} +fd ".*config" src/ -x perl -0777pe 's|openmp16|openmp32|mg' -i {} +fd ".*config" src/ -x perl -0777pe 's|cpus = 16|cpus = 32|mg' -i {} diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config index 7a3302d7d6068d7e2bd71481064b99a91dc9da4f..7642dec3eebc918e1ce97c6fbd1135daf6805f66 100644 --- a/src/nf_modules/bedtools/fasta_from_bed.config +++ b/src/nf_modules/bedtools/fasta_from_bed.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: fasta_from_bed { @@ -29,7 +29,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -46,7 +46,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config index c67cef25d2ad1a3d9c01a93ce37b6c6e1ce6f74f..0fa19189ab96dc855b13ac080a6db39d13f0c57e 100644 --- a/src/nf_modules/bowtie/indexing.config +++ b/src/nf_modules/bowtie/indexing.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: index_fasta { @@ -27,10 +27,10 @@ profiles { executor = "sge" clusterOptions = "-cwd -V" memory = "20GB" - cpus = 16 + cpus = 32 time = "12h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -47,7 +47,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config index ac4c35e46a11ddab8fe6c6dc33f67dd09e99eeae..b29cc8debc4cdb20308f59e39f95e6fbcd0daecf 100644 --- a/src/nf_modules/bowtie/mapping_paired.config +++ b/src/nf_modules/bowtie/mapping_paired.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: mapping_fastq { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/bowtie/1.2.2" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -47,7 +47,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config index ac4c35e46a11ddab8fe6c6dc33f67dd09e99eeae..b29cc8debc4cdb20308f59e39f95e6fbcd0daecf 100644 --- a/src/nf_modules/bowtie/mapping_single.config +++ b/src/nf_modules/bowtie/mapping_single.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: mapping_fastq { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/bowtie/1.2.2" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -47,7 +47,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config index dd1e5e0648c2c38159cce2841d2201bd05d79e29..2f37d6929b0607b0e0300e682a640d89256904d5 100644 --- a/src/nf_modules/bowtie2/indexing.config +++ b/src/nf_modules/bowtie2/indexing.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: index_fasta { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "20GB" time = "12h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -47,7 +47,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config index c4b0fdd102fd74fa4151e7543e44f42ecfcb3cdf..155b3668524dc701d0aca7e8b25dfd2c04681a86 100644 --- a/src/nf_modules/bowtie2/mapping_paired.config +++ b/src/nf_modules/bowtie2/mapping_paired.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: mapping_fastq { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -47,7 +47,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config index c4b0fdd102fd74fa4151e7543e44f42ecfcb3cdf..155b3668524dc701d0aca7e8b25dfd2c04681a86 100644 --- a/src/nf_modules/bowtie2/mapping_single.config +++ b/src/nf_modules/bowtie2/mapping_single.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: mapping_fastq { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -47,7 +47,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config index 689b5fa2de7db12f2691efd89221fbaf66d7a950..12adc8e63eae5aca04d7f725ed4e775fe23530ad 100644 --- a/src/nf_modules/bwa/indexing.config +++ b/src/nf_modules/bwa/indexing.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: index_fasta { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/bwa_0.7.17" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -47,7 +47,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config index b2e198a0629c28595aaf4fedc7f83e7e5dd9232c..7fce44a33d5d0ba46dbd5bf9db3750740ae6d911 100644 --- a/src/nf_modules/bwa/mapping_paired.config +++ b/src/nf_modules/bwa/mapping_paired.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: mapping_fastq { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/bwa_0.7.17" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -47,7 +47,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config index ed42799d9cc1e9a8d3c532a61f3918d3c727cfbd..30b344cd0c5d0d9d09e03d00818b8f4034a99031 100644 --- a/src/nf_modules/cutadapt/adaptor_removal_paired.config +++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: adaptor_removal { @@ -29,7 +29,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -46,7 +46,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config index ed42799d9cc1e9a8d3c532a61f3918d3c727cfbd..30b344cd0c5d0d9d09e03d00818b8f4034a99031 100644 --- a/src/nf_modules/cutadapt/adaptor_removal_single.config +++ b/src/nf_modules/cutadapt/adaptor_removal_single.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: adaptor_removal { @@ -29,7 +29,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -46,7 +46,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config index 8c158c0e72a5927b67cf1a4c106f7e22555e1cba..397c7f5c34c874427b643a29ce09f0d8b9024573 100644 --- a/src/nf_modules/cutadapt/trimming_paired.config +++ b/src/nf_modules/cutadapt/trimming_paired.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: trimming { @@ -29,7 +29,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -46,7 +46,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config index 8c158c0e72a5927b67cf1a4c106f7e22555e1cba..397c7f5c34c874427b643a29ce09f0d8b9024573 100644 --- a/src/nf_modules/cutadapt/trimming_single.config +++ b/src/nf_modules/cutadapt/trimming_single.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: trimming { @@ -29,7 +29,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -46,7 +46,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config index 2cbf9d68a467a99ed2bdd59db667c7b5533c42be..6d26a3e52f9915580c5b2d1bd9b88aae3ee84a10 100644 --- a/src/nf_modules/deeptools/bam_to_bigwig.config +++ b/src/nf_modules/deeptools/bam_to_bigwig.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: index_bam { @@ -34,22 +34,22 @@ profiles { conda = "$baseDir/.conda_envs/sambamba_0.6.7" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } withName: bam_to_bigwig { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" module = "deeptools/3.0.2" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -67,7 +67,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } withName: bam_to_bigwig { container = "lbmc/deeptools:3.0.2" @@ -78,7 +78,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config index d1c05456c37ccf67b9a21ff48da719b45060aa50..5a8c413559562cfbeddbd9d5f164128ab5d398e6 100644 --- a/src/nf_modules/deeptools/compute_matrix.config +++ b/src/nf_modules/deeptools/compute_matrix.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: compute_matrix { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/deeptools_3.0.2" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config index c10e0edc66a119775a2600b2890eede8824a9468..67b36ba408c2efb311a23cf20904e5e05ae23a28 100644 --- a/src/nf_modules/deeptools/plot_profile.config +++ b/src/nf_modules/deeptools/plot_profile.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: plot_profile { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/deeptools_3.0.2" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config index d2ef420f462fcc3b43dfd29b3c24baeb0afc86db..becedca34c171f3222138121e981a7a7d46604e7 100644 --- a/src/nf_modules/fastp/fastp_paired.config +++ b/src/nf_modules/fastp/fastp_paired.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: fastp_fastq { @@ -29,7 +29,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -47,7 +47,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config index d2ef420f462fcc3b43dfd29b3c24baeb0afc86db..becedca34c171f3222138121e981a7a7d46604e7 100644 --- a/src/nf_modules/fastp/fastp_single.config +++ b/src/nf_modules/fastp/fastp_single.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: fastp_fastq { @@ -29,7 +29,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -47,7 +47,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config index 743c85ec616152e94ee9da40e254c8a6a826416a..eddcc94bbe4d2fea107eb138c641653fcbb42169 100644 --- a/src/nf_modules/fastqc/fastqc_paired.config +++ b/src/nf_modules/fastqc/fastqc_paired.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: fastqc_fastq { @@ -29,7 +29,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -47,7 +47,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config index 743c85ec616152e94ee9da40e254c8a6a826416a..eddcc94bbe4d2fea107eb138c641653fcbb42169 100644 --- a/src/nf_modules/fastqc/fastqc_single.config +++ b/src/nf_modules/fastqc/fastqc_single.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: fastqc_fastq { @@ -29,7 +29,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -47,7 +47,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config index ab38148c140ddf8691df3b1ded842c328ad9f027..e726418fe771a01f63872d09eb3a07e4407cb47f 100644 --- a/src/nf_modules/hisat2/indexing.config +++ b/src/nf_modules/hisat2/indexing.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: index_fasta { @@ -27,10 +27,10 @@ profiles { executor = "sge" clusterOptions = "-cwd -V" memory = "20GB" - cpus = 16 + cpus = 32 time = "12h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config index b3e4df5797cd3b98c7c28632f44944f50e5188fc..964db5213282012246a0fbfe63332abd37f53e5b 100644 --- a/src/nf_modules/hisat2/mapping_paired.config +++ b/src/nf_modules/hisat2/mapping_paired.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: mapping_fastq { @@ -27,10 +27,10 @@ profiles { executor = "sge" clusterOptions = "-cwd -V" memory = "20GB" - cpus = 16 + cpus = 32 time = "12h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config index b3e4df5797cd3b98c7c28632f44944f50e5188fc..964db5213282012246a0fbfe63332abd37f53e5b 100644 --- a/src/nf_modules/hisat2/mapping_single.config +++ b/src/nf_modules/hisat2/mapping_single.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: mapping_fastq { @@ -27,10 +27,10 @@ profiles { executor = "sge" clusterOptions = "-cwd -V" memory = "20GB" - cpus = 16 + cpus = 32 time = "12h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config index 2eebc16c3af08c2bcf5924b42a6ed346a421a4f4..40f27a3a64da9be46c2ccebdb8c4bf9fbb8bf5e0 100644 --- a/src/nf_modules/htseq/htseq.config +++ b/src/nf_modules/htseq/htseq.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: sort_bam { @@ -37,7 +37,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } withName: counting { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" @@ -47,7 +47,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -65,7 +65,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } withName: counting { container = "lbmc/htseq:0.11.2" @@ -76,7 +76,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config index 3ca188a0d614661f971529630df0870617b39f92..14dd1ade20334c7cdd140d4e73157e2a5bdb259d 100644 --- a/src/nf_modules/kallisto/indexing.config +++ b/src/nf_modules/kallisto/indexing.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName index_fasta { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/kallisto_0.44.0" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config index 04b61fea005056198f09c2a6b8418608dd1c94b4..7fdd1dcd5013e25dd8d494a007883ca90589dd4f 100644 --- a/src/nf_modules/kallisto/mapping_paired.config +++ b/src/nf_modules/kallisto/mapping_paired.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: mapping_fastq { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/kallisto_0.44.0" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config index 04b61fea005056198f09c2a6b8418608dd1c94b4..7fdd1dcd5013e25dd8d494a007883ca90589dd4f 100644 --- a/src/nf_modules/kallisto/mapping_single.config +++ b/src/nf_modules/kallisto/mapping_single.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: mapping_fastq { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/kallisto_0.44.0" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config index 35186c52c4701124f937a5daa625e72e8cb0a85e..7c4c8500a49bab485edf43d8a53238ecd7c4e470 100644 --- a/src/nf_modules/macs2/peak_calling.config +++ b/src/nf_modules/macs2/peak_calling.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: peak_calling { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/macs2_2.1.2" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config index 1cb17b7cd1cdb912c835877e043d1af80f34002d..d0202652466b072d53eb2b08fa4b76ac7411eebf 100644 --- a/src/nf_modules/multiqc/multiqc_paired.config +++ b/src/nf_modules/multiqc/multiqc_paired.config @@ -1,7 +1,7 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: fastqc_fastq { @@ -39,8 +39,8 @@ profiles { memory = "5GB" time = "6h" queueSize = 1.70 - pollInterval = '60sec' - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + pollInterval = "60sec" + queue = "monointeldeb128" } withName: multiqc { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" @@ -51,8 +51,8 @@ profiles { memory = "5GB" time = "6h" queueSize = 1.70 - pollInterval = '60sec' - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + pollInterval = "60sec" + queue = "monointeldeb128" } } } @@ -70,7 +70,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } withName: multiqc { container = "lbmc/multiqc:1.7" @@ -81,7 +81,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config index ba1bbe7c996ec4f7ae9ce1e2c4cefbcb883087b1..301dde8bcc0a91d04b3f3f9f77b79e7ac4eec13e 100644 --- a/src/nf_modules/multiqc/multiqc_single.config +++ b/src/nf_modules/multiqc/multiqc_single.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: fastqc_fastq { @@ -38,8 +38,8 @@ profiles { memory = "5GB" time = "6h" queueSize = 1.70 - pollInterval = '60sec' - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + pollInterval = "60sec" + queue = "monointeldeb128" } withName: multiqc { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" @@ -50,8 +50,8 @@ profiles { memory = "5GB" time = "6h" queueSize = 1.70 - pollInterval = '60sec' - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + pollInterval = "60sec" + queue = "monointeldeb128" } } } @@ -69,7 +69,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } withName: multiqc { container = "lbmc/multiqc:1.7" @@ -80,7 +80,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config index 4a500bb9c52cecf86bca242df15b8024f65fe632..0372788c856c0ddb9bdabb8660686c9ab9e85ac4 100644 --- a/src/nf_modules/music/peak_calling_single.config +++ b/src/nf_modules/music/peak_calling_single.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: compute_mappability { @@ -45,7 +45,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } withName: music_preprocessing { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" @@ -55,7 +55,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } withName: music_computation{ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" @@ -65,7 +65,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -83,7 +83,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } withName: music_preprocessing { container = "lbmc/music:6613c53" @@ -94,7 +94,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } withName: music_computation{ container = "lbmc/music:6613c53" @@ -105,7 +105,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config index d5d3c7814b253b5869e799f7268f6985972d3d2c..c2c06001c3436018155887b1961f7bfd06f9ae7a 100644 --- a/src/nf_modules/rsem/indexing.config +++ b/src/nf_modules/rsem/indexing.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: index_fasta { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/rsem_1.3.0" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config index bde03fc98ab828ebc58ee268a2dd9b1fe342f77b..fd73ae6622e64f6abb563c212e329e1286a18c26 100644 --- a/src/nf_modules/rsem/quantification_paired.config +++ b/src/nf_modules/rsem/quantification_paired.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: mapping_fastq { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/rsem_1.3.0" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config index bde03fc98ab828ebc58ee268a2dd9b1fe342f77b..fd73ae6622e64f6abb563c212e329e1286a18c26 100644 --- a/src/nf_modules/rsem/quantification_single.config +++ b/src/nf_modules/rsem/quantification_single.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: mapping_fastq { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/rsem_1.3.0" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config index 3a20b7e120fceb5532a82555829a84e3fe5a435a..c3d12b70898b790ea2cbe33a3989cd5c8c84588b 100644 --- a/src/nf_modules/sambamba/index_bams.config +++ b/src/nf_modules/sambamba/index_bams.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: index_bam { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/sambamba_0.6.9" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config index 8612de4aacf04c0ee6eb41e318b118cf3e72b4a6..1db926f701ff0c5f2bab741c4631066f0165b426 100644 --- a/src/nf_modules/sambamba/sort_bams.config +++ b/src/nf_modules/sambamba/sort_bams.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: sort_bam { @@ -29,8 +29,8 @@ profiles { cpus = 4 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config index 4ce0bcb06a61c5941223381c16f1996c48ee67b1..1ec31c3ea52c4c1b825d8a8a7b408e8eb468e371 100644 --- a/src/nf_modules/sambamba/split_bams.config +++ b/src/nf_modules/sambamba/split_bams.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: split_bam { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/sambamba_0.6.9" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config index 66f3051148ad1bcfddf4ca73c85b2b9040a3c963..10c1649ec60f8c491d6f119eda18f792b7ed0535 100644 --- a/src/nf_modules/samblaster/dedup_sams.config +++ b/src/nf_modules/samblaster/dedup_sams.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: dedup_sam { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/samblaster_0.1.24" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config index b2cdd8e5202f179833e877e8346430e01826fc17..46933f1d8264266cfa7f03726ff745c649785747 100644 --- a/src/nf_modules/samtools/filter_bams.config +++ b/src/nf_modules/samtools/filter_bams.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: filter_bam { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/samtools_1.7" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config index 3e2156e16ee72fddb0b317c0dd22e3342fbe1cd8..438f8379875b9b956d8f91dfa2a6bf276b710291 100644 --- a/src/nf_modules/samtools/index_bams.config +++ b/src/nf_modules/samtools/index_bams.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: index_bam { @@ -29,7 +29,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -47,7 +47,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config index dd7cd38b2fe475ad409444ad2406e08c6a21b6cb..81371fb516324ee61c1d0783e325787d5815c612 100644 --- a/src/nf_modules/samtools/sort_bams.config +++ b/src/nf_modules/samtools/sort_bams.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: sort_bam { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/samtools_1.7" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config index 6c8ca3e963019002889a8f1ee3c3bb1166df7737..837fe88d26f7c2ce38ed132fde92aa228ce51e78 100644 --- a/src/nf_modules/samtools/split_bams.config +++ b/src/nf_modules/samtools/split_bams.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: split_bam { @@ -29,7 +29,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -47,7 +47,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config index e6e80c5dffe098e1e893af480600a6ce40661d03..4c6516975ebe77a72aefad962e781cb5d0edadbc 100644 --- a/src/nf_modules/sratoolkit/fastqdump.config +++ b/src/nf_modules/sratoolkit/fastqdump.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: fastq_dump { @@ -29,7 +29,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -47,7 +47,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/star/indexing.config b/src/nf_modules/star/indexing.config index 34683657e3856d700dfc357591f46477598de70b..cef16406d014c1a1a7bf8a83b73baf5a69cd0b63 100644 --- a/src/nf_modules/star/indexing.config +++ b/src/nf_modules/star/indexing.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: index_fasta { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/star_2.7.3a" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "20GB" time = "12h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -47,7 +47,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/star/mapping_paired.config b/src/nf_modules/star/mapping_paired.config index 615404c4928c2281722ad15b50055b37eddfb7aa..6f8f8048d3f14af0a1ee89bf2ab8dfd4866ac5fc 100644 --- a/src/nf_modules/star/mapping_paired.config +++ b/src/nf_modules/star/mapping_paired.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: mapping_fastq { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/star_2.7.3a" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -47,7 +47,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/star/mapping_single.config b/src/nf_modules/star/mapping_single.config index 615404c4928c2281722ad15b50055b37eddfb7aa..6f8f8048d3f14af0a1ee89bf2ab8dfd4866ac5fc 100644 --- a/src/nf_modules/star/mapping_single.config +++ b/src/nf_modules/star/mapping_single.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: mapping_fastq { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/star_2.7.3a" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -47,7 +47,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config index 68147001c4c8d630210e9c617b193d977212721c..ef2aa7e555a8d661b80a4819889f955150d15efb 100644 --- a/src/nf_modules/subread/subread.config +++ b/src/nf_modules/subread/subread.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: sort_bam { @@ -37,7 +37,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } withName: counting { beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" @@ -47,7 +47,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } } } @@ -65,7 +65,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } withName: counting { container = "lbmc/subread:1.6.4" @@ -76,7 +76,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config index a9f28632bc1552a9d497f9ddc8b7f73e26b9f6fe..87f7f7f949a373e857d75f297a74925a72352496 100644 --- a/src/nf_modules/urqt/trimming_paired.config +++ b/src/nf_modules/urqt/trimming_paired.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: trimming { @@ -27,10 +27,10 @@ profiles { executor = "sge" clusterOptions = "-cwd -V" memory = "5GB" - cpus = 16 + cpus = 32 time = "12h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config index 012b3f3afb518677d0aae318979701d32861cca5..c2b5757ea515088634987ec55c29e9afe593ba12 100644 --- a/src/nf_modules/urqt/trimming_single.config +++ b/src/nf_modules/urqt/trimming_single.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: trimming { @@ -26,11 +26,11 @@ profiles { conda = "$baseDir/.conda_envs/urqt_d62c1f8" executor = "sge" clusterOptions = "-cwd -V" - cpus = 16 + cpus = 32 memory = "5GB" time = "12h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -48,7 +48,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/solution_RNASeq.config b/src/solution_RNASeq.config index 3e8ba47bdb12f98c134ca4ebf96a2593d6ba6c2c..a8eb7758ef98d4e0097047417d58d6136a510e58 100644 --- a/src/solution_RNASeq.config +++ b/src/solution_RNASeq.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: adaptor_removal { @@ -61,7 +61,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128' + queue = "monointeldeb128" } withName: trimming { beforeScript = "source $baseDir/.conda_psmn.sh" @@ -71,8 +71,8 @@ profiles { cpus = 32 memory = "30GB" time = "24h" - queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D' - penv = 'openmp32' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } withName: fasta_from_bed { @@ -83,7 +83,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128' + queue = "monointeldeb128" } withName: index_fasta { beforeScript = "source $baseDir/.conda_psmn.sh" @@ -93,8 +93,8 @@ profiles { cpus = 32 memory = "30GB" time = "24h" - queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D' - penv = 'openmp32' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } withName: mapping_fastq { beforeScript = "source $baseDir/.conda_psmn.sh" @@ -104,8 +104,8 @@ profiles { cpus = 32 memory = "30GB" time = "24h" - queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D' - penv = 'openmp32' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -122,7 +122,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } withName: trimming { container = "lbmc/urqt:d62c1f8" @@ -133,7 +133,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } withName: fasta_from_bed { container = "lbmc/bedtools:2.25.0" @@ -143,7 +143,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } withName: index_fasta { container = "lbmc/kallisto:0.44.0" @@ -154,7 +154,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } withName: mapping_fastq { container = "lbmc/kallisto:0.44.0" @@ -165,7 +165,7 @@ profiles { clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ " cpus = 1 - queue = 'huge' + queue = "huge" } } } diff --git a/src/training_dataset.config b/src/training_dataset.config index 226acd9fd45046d7e24d829de16447d81873c8d4..734a7410c3f3d2425a98b2f1462faee929dc68e1 100644 --- a/src/training_dataset.config +++ b/src/training_dataset.config @@ -1,6 +1,6 @@ profiles { docker { - docker.temp = 'auto' + docker.temp = "auto" docker.enabled = true process { withName: build_synthetic_bed { @@ -125,7 +125,7 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } withName: fasta_from_bed { beforeScript = "source $baseDir/.conda_psmn.sh" @@ -135,106 +135,106 @@ profiles { cpus = 1 memory = "20GB" time = "12h" - queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' + queue = "monointeldeb128" } withName: index_fasta { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1" executor = "sge" clusterOptions = "-m e -cwd -V" - cpus = 16 + cpus = 32 memory = "20GB" time = "12h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } withName: mapping_fastq_paired { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1" executor = "sge" clusterOptions = "-m e -cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } withName: bam_2_fastq_paired { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/samtools_1.7" executor = "sge" clusterOptions = "-m e -cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } withName: sort_bam_paired { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/samtools_1.7" executor = "sge" clusterOptions = "-m e -cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } withName: index_bam_paired { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/samtools_1.7" executor = "sge" clusterOptions = "-m e -cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } withName: mapping_fastq_single { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1" executor = "sge" clusterOptions = "-m e -cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } withName: bam_2_fastq_single { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/samtools_1.7" executor = "sge" clusterOptions = "-m e -cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } withName: sort_bam_single { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/samtools_1.7" executor = "sge" clusterOptions = "-m e -cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } withName: index_bam_single { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/samtools_1.7" executor = "sge" clusterOptions = "-m e -cwd -V" - cpus = 16 + cpus = 32 memory = "30GB" time = "24h" - queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' - penv = 'openmp16' + queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" + penv = "openmp32" } } } @@ -251,7 +251,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } process{ @@ -263,7 +263,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } withName: fasta_from_bed { container = "lbmc/bedtools:2.25.0" @@ -273,7 +273,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } withName: index_fasta { container = "lbmc/bowtie2:2.3.4.1" @@ -283,7 +283,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } withName: mapping_fastq_paired { container = "lbmc/bowtie2:2.3.4.1" @@ -293,7 +293,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } withName: bam_2_fastq_paired { container = "lbmc/samtools:1.7" @@ -303,7 +303,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } withName: sort_bam_paired { container = "lbmc/samtools:1.7" @@ -313,7 +313,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } withName: index_bam_paired { container = "lbmc/samtools:1.7" @@ -323,7 +323,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } withName: mapping_fastq_single { container = "lbmc/bowtie2:2.3.4.1" @@ -333,7 +333,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } withName: bam_2_fastq_single { container = "lbmc/samtools:1.7" @@ -343,7 +343,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } withName: sort_bam_single { container = "lbmc/samtools:1.7" @@ -353,7 +353,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } withName: index_bam_single { container = "lbmc/samtools:1.7" @@ -363,7 +363,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 - queue = 'huge' + queue = "huge" } } }