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Commit 90a09fd4 authored by nservant's avatar nservant
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fix first batch of revision

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conf/curie.config deleted 100644 → 0
+ 0
− 16
View file @ 97d3d5da
singularity {
enabled = false
}
process {
executor = 'pbs'
queue = params.queue
//beforeScript = 'export PATH=/bioinfo/pipelines/sandbox/dev/nfcore/rnaseq/modules/conda/envs/nf-core-rnaseq-1.2/bin:$PATH'
}
params {
clusterOptions = false
max_memory = 128.GB
max_cpus = 4
max_time = 240.h
}
conf/multiqc_config.yaml deleted 100644 → 0
+ 0
− 7
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report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/hic" target="_blank">nf-core/hic</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://github.com/nf-core/hic" target="_blank">documentation</a>.
report_section_order:
nf-core/hic-software-versions:
order: -1000
docs/README.md
+ 5
− 5
View file @ 90a09fd4
......@@ -2,11 +2,11 @@
The nf-core/hic documentation is split into the following files:
1. [Installation](installation.md)
1. [Installation](https://nf-co.re/usage/installation)
2. Pipeline configuration
* [Local installation](configuration/local.md)
* [Adding your own system](configuration/adding_your_own.md)
* [Reference genomes](configuration/reference_genomes.md)
* [Local installation](https://nf-co.re/usage/local_installation)
* [Adding your own system config](https://nf-co.re/usage/adding_own_config)
* [Reference genomes](https://nf-co.re/usage/reference_genomes)
3. [Running the pipeline](usage.md)
4. [Output and how to interpret the results](output.md)
5. [Troubleshooting](troubleshooting.md)
5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
main.nf
+ 21
− 19
View file @ 90a09fd4
......@@ -26,7 +26,7 @@ def helpMessage() {
-profile Configuration profile to use. Can use multiple (comma separated)
Available: conda, docker, singularity, awsbatch, test and more.
References: If not specified in the configuration file or you wish to overwrite any of the references.
References If not specified in the configuration file or you wish to overwrite any of the references.
--genome Name of iGenomes reference
--bwt2_index Path to Bowtie2 index
--fasta Path to Fasta reference
......@@ -35,12 +35,17 @@ def helpMessage() {
--saveReference Save reference genome to output folder. Default: False
--saveAlignedIntermediates Save intermediates alignment files. Default: False
Options:
Alignments
--bwt2_opts_end2end Options for bowtie2 end-to-end mappinf (first mapping step). See hic.config for default.
--bwt2_opts_trimmed Options for bowtie2 mapping after ligation site trimming. See hic.config for default.
--min_mapq Minimum mapping quality values to consider. Default: 10
--restriction_site Cutting motif(s) of restriction enzyme(s) (comma separated). Default: 'A^AGCTT'
--ligation_site Ligation motifs to trim (comma separated). Default: 'AAGCTAGCTT'
--rm_singleton Remove singleton reads. Default: true
--rm_multi Remove multi-mapped reads. Default: true
--rm_dup Remove duplicates. Default: true
Contacts calling
--min_restriction_fragment_size Minimum size of restriction fragments to consider. Default: None
--max_restriction_framgnet_size Maximum size of restriction fragmants to consider. Default: None
--min_insert_size Minimum insert size of mapped reads to consider. Default: None
......@@ -48,32 +53,29 @@ def helpMessage() {
--saveInteractionBAM Save BAM file with interaction tags (dangling-end, self-circle, etc.). Default: False
--dnase Run DNase Hi-C mode. All options related to restriction fragments are not considered. Default: False
--min_cis_dist Minimum intra-chromosomal distance to consider. Default: None
--rm_singleton Remove singleton reads. Default: true
--rm_multi Remove multi-mapped reads. Default: true
--rm_dup Remove duplicates. Default: true
Contact maps
--bin_size Bin size for contact maps (comma separated). Default: '1000000,500000'
--ice_max_iter Maximum number of iteration for ICE normalization. Default: 100
--ice_filter_low_count_perc Percentage of low counts columns/rows to filter before ICE normalization. Default: 0.02
--ice_filter_high_count_perc Percentage of high counts columns/rows to filter before ICE normalization. Default: 0
--ice_eps Convergence criteria for ICE normalization. Default: 0.1
Other options:
--splitFastq Size of read chuncks to use to speed up the workflow. Default: None
--outdir The output directory where the results will be saved. Default: './results'
--email Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. Default: None
-name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic. Default: None
Step options:
Workflow
--skip_maps Skip generation of contact maps. Useful for capture-C. Default: False
--skip_ice Skip ICE normalization. Default: False
--skip_cool Skip generation of cool files. Default: False
--skip_multiQC Skip MultiQC. Default: False
AWSBatch options:
Other
--splitFastq Size of read chuncks to use to speed up the workflow. Default: None
--outdir The output directory where the results will be saved. Default: './results'
--email Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. Default: None
-name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic. Default: None
AWSBatch
--awsqueue The AWSBatch JobQueue that needs to be set when running on AWSBatch
--awsregion The AWS Region for your AWS Batch job to run on
""".stripIndent()
......@@ -802,7 +804,7 @@ process generate_cool{
/*
* STEP 5 - MultiQC
* STEP 6 - MultiQC
*/
process multiqc {
publishDir "${params.outdir}/MultiQC", mode: 'copy'
......@@ -832,7 +834,7 @@ process multiqc {
/*
* STEP 3 - Output Description HTML
* STEP 7 - Output Description HTML
*/
process output_documentation {
publishDir "${params.outdir}/pipeline_info", mode: 'copy'
......@@ -975,14 +977,14 @@ def nfcoreHeader(){
c_cyan = params.monochrome_logs ? '' : "\033[0;36m";
c_white = params.monochrome_logs ? '' : "\033[0;37m";
return """ ${c_dim}----------------------------------------------------${c_reset}
return """ -${c_dim}--------------------------------------------------${c_reset}-
${c_green},--.${c_black}/${c_green},-.${c_reset}
${c_blue} ___ __ __ __ ___ ${c_green}/,-._.--~\'${c_reset}
${c_blue} |\\ | |__ __ / ` / \\ |__) |__ ${c_yellow}} {${c_reset}
${c_blue} | \\| | \\__, \\__/ | \\ |___ ${c_green}\\`-._,-`-,${c_reset}
${c_green}`._,._,\'${c_reset}
${c_purple} nf-core/hic v${workflow.manifest.version}${c_reset}
${c_dim}----------------------------------------------------${c_reset}
${c_purple} nf-core/atacseq v${workflow.manifest.version}${c_reset}
-${c_dim}--------------------------------------------------${c_reset}-
""".stripIndent()
}
......
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