From 0e19e4f31c0953ce064cfd685ad116fead4f3fba Mon Sep 17 00:00:00 2001
From: Nicolas Servant <nicolas.servant@curie.fr>
Date: Thu, 18 Jul 2024 11:54:40 +0200
Subject: [PATCH] [MODIF] lint

---
 modules/local/hicpro/dnase_mapping_stats.nf   |  2 +-
 subworkflows/local/compartments.nf            |  2 +-
 .../local/utils_nfcore_hic_pipeline/main.nf   | 22 +++++++++----------
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/modules/local/hicpro/dnase_mapping_stats.nf b/modules/local/hicpro/dnase_mapping_stats.nf
index 3b47154..7b5abb3 100644
--- a/modules/local/hicpro/dnase_mapping_stats.nf
+++ b/modules/local/hicpro/dnase_mapping_stats.nf
@@ -28,7 +28,7 @@ process MAPPING_STATS_DNASE {
     echo -n "global_${tag}\t" >> ${prefix}.mapstat
     samtools view -c -F 4 ${bam} >> ${prefix}.mapstat
     echo -n "local_${tag}\t0"  >> ${prefix}.mapstat
- 
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/subworkflows/local/compartments.nf b/subworkflows/local/compartments.nf
index 0ab2298..3dcd53e 100644
--- a/subworkflows/local/compartments.nf
+++ b/subworkflows/local/compartments.nf
@@ -17,7 +17,7 @@ workflow COMPARTMENTS {
             chrsize.map{it -> it[1]}.collect()
         )
         ch_versions = ch_versions.mix(COOLTOOLS_EIGSCIS.out.versions)
-        ch_comp = COOLTOOLS_EIGSCIS.out.results	
+	ch_comp = COOLTOOLS_EIGSCIS.out.results
     }
 
     if (params.compartments_caller =~ 'calder2'){
diff --git a/subworkflows/local/utils_nfcore_hic_pipeline/main.nf b/subworkflows/local/utils_nfcore_hic_pipeline/main.nf
index 94f1c28..2ba617d 100644
--- a/subworkflows/local/utils_nfcore_hic_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_hic_pipeline/main.nf
@@ -217,11 +217,11 @@ def toolCitationText() {
     def citation_text = [
             "Tools used in the workflow included:",
             "FastQC (Andrews 2010),",
-	    "Bowtie2 (Langmead 2012),",
-	    "BWA-MEM (Li 2013),",
-	    "HiC-Pro (Servant 2015),",
-	    "Pairtools (Open2C 2023),",
-	    "Cooltools (Open2C 2024),",
+            "Bowtie2 (Langmead 2012),",
+            "BWA-MEM (Li 2013),",
+            "HiC-Pro (Servant 2015),",
+            "Pairtools (Open2C 2023),",
+            "Cooltools (Open2C 2024),",
             "MultiQC (Ewels et al. 2016)",
             "."
         ].join(' ').trim()
@@ -234,12 +234,12 @@ def toolBibliographyText() {
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def reference_text = [
             "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
-	    "<li>Langmead, B., Salzberg, S. (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359. https://doi.org/10.1038/nmeth.1923</li>",
-	    "<li>Li, H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2</li>",
-	    "<li>Servant, N., Varoquaux, N., Lajoie, B.R., Viara, E., Chen, CJ., Vert, JP., Heard E., Dekker J., Barillot, E. (2015) HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol 16, 259. https://doi.org/10.1186/s13059-015-0831-x</li>",
-	    "<li>Open2C, Abdennur, N., Fudenberg, G., Flyamer, IM., Galitsyna, AA., Goloborodko, A., Imakaev, M., Venev, SV. (2023). Pairtools: from sequencing data to chromosome contacts. PloS Comput Biol. 20(5):e1012164. doi: 10.1371/journal.pcbi.1012164</li>",
-	    "<li>Open2C, Abdennur, N., Abraham, S., Fudenberg, G., Flyamer, IM., Galitsyna, AA., Goloborodko, A., Imakaev, M., Oksuz, BA., & Venev, SV. (2024). Cooltools: Enabling High-Resolution Hi-C Analysis in Python. PLoS Comput Biol. 6;20(5):e1012067. doi: 10.1371/journal.pcbi.1012067</li>",
-	    "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"	    
+            "<li>Langmead, B., Salzberg, S. (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359. https://doi.org/10.1038/nmeth.1923</li>",
+            "<li>Li, H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2</li>",
+            "<li>Servant, N., Varoquaux, N., Lajoie, B.R., Viara, E., Chen, CJ., Vert, JP., Heard E., Dekker J., Barillot, E. (2015) HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol 16, 259. https://doi.org/10.1186/s13059-015-0831-x</li>",
+            "<li>Open2C, Abdennur, N., Fudenberg, G., Flyamer, IM., Galitsyna, AA., Goloborodko, A., Imakaev, M., Venev, SV. (2023). Pairtools: from sequencing data to chromosome contacts. PloS Comput Biol. 20(5):e1012164. doi: 10.1371/journal.pcbi.1012164</li>",
+            "<li>Open2C, Abdennur, N., Abraham, S., Fudenberg, G., Flyamer, IM., Galitsyna, AA., Goloborodko, A., Imakaev, M., Oksuz, BA., & Venev, SV. (2024). Cooltools: Enabling High-Resolution Hi-C Analysis in Python. PLoS Comput Biol. 6;20(5):e1012067. doi: 10.1371/journal.pcbi.1012067</li>",
+            "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"	    
         ].join(' ').trim()
 
     return reference_text