diff --git a/workflow/rules/bamCoverage.rules b/workflow/rules/bamCoverage.rules index d812e23ddaf83740bf7f381141a3bd9bdc362a06..30c61a8095ed18e22db3c025a806363c427e7639 100644 --- a/workflow/rules/bamCoverage.rules +++ b/workflow/rules/bamCoverage.rules @@ -29,7 +29,7 @@ rule bamCoverage: output: bamCoverage_output singularity: - "rnaflow.img" + "chipflow.img" params: options = bamCoverage_options envmodules: diff --git a/workflow/rules/bed_to_gff.rules b/workflow/rules/bed_to_gff.rules index 46de44dfc08e00e45c117b50fe3d45763a4fc9a2..05ee544a72d7b398db01460cb16b087ed720f92a 100755 --- a/workflow/rules/bed_to_gff.rules +++ b/workflow/rules/bed_to_gff.rules @@ -30,7 +30,7 @@ rule bed_to_gff: output: temp(bed_to_gff_output) singularity: - "chipuana.img" + "chipflow.img" shell: """ awk 'BEGIN{{OFS="\t"}} {{print $1"\tChIPflow\tpeak\t"$2+1"\t"$3+1"\t.\t.\t.\tgene_id \"$1"_"$2"_"$3}}' {input} > {output} 2> {log} diff --git a/workflow/rules/bowtie2_index.rules b/workflow/rules/bowtie2_index.rules index 40ddf7741fc6136bfe1cdbe52f3d4b4d51f01c78..8de9a44ec7190a464ac1f4c5b58780d76db9adf8 100755 --- a/workflow/rules/bowtie2_index.rules +++ b/workflow/rules/bowtie2_index.rules @@ -28,7 +28,7 @@ rule bowtie2_index: output: bowtie2_index_output_done singularity: - "chipuana.img" + "chipflow.img" params: prefix = bowtie2_index_output_prefix log: diff --git a/workflow/rules/bowtie2_mapping.rules b/workflow/rules/bowtie2_mapping.rules index 8b212f67be73a0805308507653d8007774e65488..0694ad0d0745fef8ecaa246dfd4311d6b6e11d0b 100755 --- a/workflow/rules/bowtie2_mapping.rules +++ b/workflow/rules/bowtie2_mapping.rules @@ -30,7 +30,7 @@ rule bowtie2_mapping: sort = bowtie2_mapping_sort, bam = temp(bowtie2_mapping_bam) singularity: - "chipuana.img" + "chipflow.img" log: err = bowtie2_mapping_logs_err, out = bowtie2_mapping_logs_out diff --git a/workflow/rules/chipuanar.rules b/workflow/rules/chipuanar.rules index df497928af0ccd544e6e4b2546e9df8a3b97ee88..ae3c5dc948cf4735f4f63f9deee52a23679d6c70 100755 --- a/workflow/rules/chipuanar.rules +++ b/workflow/rules/chipuanar.rules @@ -32,7 +32,7 @@ rule chipuanar: log: chipuanar_logs singularity: - "chipuana.img" + "chipflow.img" shell: """ set +o pipefail diff --git a/workflow/rules/compute_idr.rules b/workflow/rules/compute_idr.rules index 73edb1876d07bb63319f841826bcbb61610cb09f..c9f149dc63f43c69aa44c476d71007b2dddebb71 100755 --- a/workflow/rules/compute_idr.rules +++ b/workflow/rules/compute_idr.rules @@ -29,7 +29,7 @@ rule compute_idr: idr = compute_idr_output, peak = compute_idr_output_peak singularity: - "chipuana.img" + "chipflow.img" log: compute_idr_log params: diff --git a/workflow/rules/cutadapt.rules b/workflow/rules/cutadapt.rules index 76b83a744158a10897a0aeaf57ce55e9c79094db..b0de6e074ab5ca25c37cf2bc92022fb75fe171eb 100755 --- a/workflow/rules/cutadapt.rules +++ b/workflow/rules/cutadapt.rules @@ -36,7 +36,7 @@ rule cutadapt: min = cutadapt_min, qual = cutadapt_qual singularity: - "chipuana.img" + "chipflow.img" threads: config['adapters']['threads'] log: cutadapt_log diff --git a/workflow/rules/fastqc.rules b/workflow/rules/fastqc.rules index 267c26af086b52caa59e1f1d8c39e4c2d0a6e4d8..7a642f92c401c964548c2127fb803f53685e964b 100755 --- a/workflow/rules/fastqc.rules +++ b/workflow/rules/fastqc.rules @@ -27,7 +27,7 @@ rule fastqc: output: touch(fastqc_output_done) singularity: - "chipuana.img" + "chipflow.img" params: wkdir = fastqc_wkdir, kargs = config['fastqc']['options'] diff --git a/workflow/rules/feature_counts.rules b/workflow/rules/feature_counts.rules index 23f82d509aaeef94aba673fe6ebbdff471daa828..e48fbeba5d3ea804b0c93e7e625530af7d373d9e 100755 --- a/workflow/rules/feature_counts.rules +++ b/workflow/rules/feature_counts.rules @@ -27,9 +27,8 @@ rule feature_counts: gff = feature_counts_gff output: feature_counts_output_count - singularity: - "chipuana.img" + "chipflow.img" params: mapp = feature_counts_options, input = feature_counts_optional_input diff --git a/workflow/rules/intersectionApproach.rules b/workflow/rules/intersectionApproach.rules index a527fc186170b14ee54ac0b19e24c6668f1c8f30..329c96c7b9b8eb54839ed15943933724fc67239a 100755 --- a/workflow/rules/intersectionApproach.rules +++ b/workflow/rules/intersectionApproach.rules @@ -31,7 +31,7 @@ rule intersectionApproach: output: intersectionApproach_output singularity: - "chipuana.img" + "chipflow.img" params: overlap = intersectionApproach_overlap shell: diff --git a/workflow/rules/macs2.rules b/workflow/rules/macs2.rules index a34b589cd1aada65faf213f64b173a6f6b580757..75e17db55eaa16103f1585a9c2ae8d3acb1878c3 100755 --- a/workflow/rules/macs2.rules +++ b/workflow/rules/macs2.rules @@ -40,7 +40,7 @@ rule macs2: output: macs2_output singularity: - "chipuana.img" + "chipflow.img" shell: """ set +o pipefail diff --git a/workflow/rules/mark_duplicates.rules b/workflow/rules/mark_duplicates.rules index 35b13033a40a378a47dd44a5c1397f4e6a222025..65154ebbcdd6c734c2da6a1c636b3289e76d6eab 100755 --- a/workflow/rules/mark_duplicates.rules +++ b/workflow/rules/mark_duplicates.rules @@ -29,7 +29,7 @@ rule mark_duplicates: bam = mark_duplicates_output, metrics = mark_duplicates_metrics singularity: - "chipuana.img" + "chipflow.img" log: out = mark_duplicates_log_std, err = mark_duplicates_log_err diff --git a/workflow/rules/multiqc.rules b/workflow/rules/multiqc.rules index fc04a178775ffac4dd3e470b872edbe2678c5016..6448889ec30b2fb4408b09d6f0dd70124c4e13cb 100755 --- a/workflow/rules/multiqc.rules +++ b/workflow/rules/multiqc.rules @@ -30,7 +30,7 @@ rule multiqc: output: multiqc_output singularity: - "chipuana.img" + "chipflow.img" params: inputdir = multiqc_input_dir, options = multiqc_options, diff --git a/workflow/rules/preIDR_PPR.rules b/workflow/rules/preIDR_PPR.rules index d465a79ca1b544d5803c63b7afe940dd9b8d8259..7ace16c8d1146dd6573a16266d20a750a10e5aa9 100755 --- a/workflow/rules/preIDR_PPR.rules +++ b/workflow/rules/preIDR_PPR.rules @@ -30,7 +30,7 @@ rule preIDR_PPR: output: preIDR_PPR_output singularity: - "chipuana.img" + "chipflow.img" shell: """ set +o pipefail diff --git a/workflow/rules/preIDR_Pool.rules b/workflow/rules/preIDR_Pool.rules index c69e56d13cb874903b2a4ba59a25de595f099f3f..6fcd05cdc2c79080aaa11c7ac739deddea437aec 100755 --- a/workflow/rules/preIDR_Pool.rules +++ b/workflow/rules/preIDR_Pool.rules @@ -30,7 +30,7 @@ rule preIDR_pool: output: preIDR_pool_output singularity: - "chipuana.img" + "chipflow.img" shell: """ set +o pipefail diff --git a/workflow/rules/preIDR_SPR.rules b/workflow/rules/preIDR_SPR.rules index 8c0fdf02552ceb13005f09216c93dc174c34a29e..9e0f2d57f29899c2ad63276fd90cf5c6505b6f8c 100755 --- a/workflow/rules/preIDR_SPR.rules +++ b/workflow/rules/preIDR_SPR.rules @@ -30,7 +30,7 @@ rule preIDR_SPR: output: preIDR_SPR_output singularity: - "chipuana.img" + "chipflow.img" shell: """ set +o pipefail diff --git a/workflow/rules/remove_blacklist.rules b/workflow/rules/remove_blacklist.rules index 75facd20996c980ecb331eed9b929b70ca652718..79b4dcbc3a5939750789b015a6cb00ddba331abc 100755 --- a/workflow/rules/remove_blacklist.rules +++ b/workflow/rules/remove_blacklist.rules @@ -27,7 +27,7 @@ rule remove_blacklist: output: bam = remove_blacklist_output singularity: - "chipuana.img" + "chipflow.img" log: out = remove_blacklist_log_std, err = remove_blacklist_log_err diff --git a/workflow/rules/select_peaks.rules b/workflow/rules/select_peaks.rules index d0f692a3af7f3dca971477e08cd8fc29e5ffb11d..e0f9a1f3adaf90ccd638976bedc53da99789704b 100755 --- a/workflow/rules/select_peaks.rules +++ b/workflow/rules/select_peaks.rules @@ -32,7 +32,7 @@ rule select_peaks: output: select_peaks_output singularity: - "chipuana.img" + "chipflow.img" shell: """ set +o pipefail diff --git a/workflow/rules/spp.rules b/workflow/rules/spp.rules index 4b55e583054cf1226341d9d903cc0d29cc3da4d2..73bcce303a4cbe08d30563ac3d1d856a50114d2a 100755 --- a/workflow/rules/spp.rules +++ b/workflow/rules/spp.rules @@ -31,7 +31,7 @@ rule spp: params: tmpdir = spp_tmpdir singularity: - "chipuana.img" + "chipflow.img" log: out = spp_log_std, err = spp_log_err diff --git a/workflow/rules/union_peaks.rules b/workflow/rules/union_peaks.rules index 17b7093f66d7fd91b955fb56fb3e6e19e4e90d36..a4c1e9cb1b292e07ebd7272c45c717ad715a47ca 100755 --- a/workflow/rules/union_peaks.rules +++ b/workflow/rules/union_peaks.rules @@ -29,7 +29,7 @@ rule union_peaks: output: union_peaks_output singularity: - "chipuana.img" + "chipflow.img" shell: """