diff --git a/conf/curie.config b/conf/curie.config
deleted file mode 100644
index ab85a2d9d778ac3ca875a273e9bbcb7eb966253d..0000000000000000000000000000000000000000
--- a/conf/curie.config
+++ /dev/null
@@ -1,16 +0,0 @@
-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
-}
diff --git a/conf/multiqc_config.yaml b/conf/multiqc_config.yaml
deleted file mode 100644
index f2a738c43be4dae15db5075017559607c66c0542..0000000000000000000000000000000000000000
--- a/conf/multiqc_config.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-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
diff --git a/docs/README.md b/docs/README.md
index d7dbdac40b9452baa3d7d7747d264077276fb679..e160867d029e09c793168dd764f8a0ea01dcbd59 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -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)
diff --git a/main.nf b/main.nf
index 31f73a8549e76b246fe05981c0c2735b5605090e..0871e66103a07faf5a02df7e3a6136f24a2e2c7e 100644
--- a/main.nf
+++ b/main.nf
@@ -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()
}