From e0ad2706e96f2a777fd26777e91d2333ef2c610c Mon Sep 17 00:00:00 2001
From: Nicolas MANOSALVA PEREZ <niman@psb.ugent.be>
Date: Thu, 21 Sep 2023 10:38:31 +0200
Subject: [PATCH 01/15] remove comment miniac_gw script getStats process

---
 workflows/miniac_gw.nf | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/workflows/miniac_gw.nf b/workflows/miniac_gw.nf
index 16c61bb..62f3533 100755
--- a/workflows/miniac_gw.nf
+++ b/workflows/miniac_gw.nf
@@ -51,12 +51,6 @@ process getStats {
    script:
 
    """
-   #bedmap --delim '\t' --fraction-ref 0.5 --echo --echo-map-id --skip-unmapped $gw_motmaps $shuffled_real_acr | awk '{n=split(\$0,a,";"); split(a[1],b,"\t"); print b[4], b[5]} n>1 {for (i=2;i<=n;i++) print b[4], a[i]}' | sort | uniq -c > ${shuffled_real_acr.baseName}_motif_int_data.txt
-
-   #bedmap --delim '\t' --fraction-either 0.5 --echo --echo-map-id --skip-unmapped $gw_motmaps $shuffled_real_acr | awk '{n=split(\$0,a,";"); split(a[1],b,"\t"); print b[4], b[5]} n>1 {for (i=2;i<=n;i++) print b[4], a[i]}' | sort | uniq -c > ${shuffled_real_acr.baseName}_motif_int_data.txt
-
-   #bedmap --delim '\t' --bp-ovr 5 --echo --echo-map-id --skip-unmapped $gw_motmaps $shuffled_real_acr | awk '{n=split(\$0,a,";"); split(a[1],b,"\t"); print b[4], b[5]} n>1 {for (i=2;i<=n;i++) print b[4], a[i]}' | sort | uniq -c > ${shuffled_real_acr.baseName}_motif_int_data.txt
-
    bedmap --delim '\t' --echo --echo-map-id --skip-unmapped $gw_motmaps $shuffled_real_acr | awk '{n=split(\$0,a,";"); split(a[1],b,"\t"); print b[4], b[5]} n>1 {for (i=2;i<=n;i++) print b[4], a[i]}' | sort | uniq -c > ${shuffled_real_acr.baseName}_motif_int_data.txt
 
    num_peaks=\$(grep -c "real_ints" $shuffled_real_acr)

From d127597bb3359020e35380810202b094140e3d68 Mon Sep 17 00:00:00 2001
From: Herman DE BEUKELAER <hebeu@midas23.psblocal>
Date: Thu, 21 Sep 2023 11:34:59 +0200
Subject: [PATCH 02/15] Remove code duplication in main workflow

---
 mini_ac.nf | 117 ++++++++++++++---------------------------------------
 1 file changed, 31 insertions(+), 86 deletions(-)

diff --git a/mini_ac.nf b/mini_ac.nf
index 5774729..e4a2776 100755
--- a/mini_ac.nf
+++ b/mini_ac.nf
@@ -7,99 +7,44 @@ workflow MINIAC {
 
     params.OBO_file = "$projectDir/data/ontologies/go.obo"
 
-    if (params.mode == "genome_wide" && params.species == "maize_v4") {
-
-        params.MotMapsFile_gw = "$projectDir/data/zma_v4/zma_v4_genome_wide_motif_mappings.bed"
-        params.Non_cod_genome = "$projectDir/data/zma_v4/zma_v4_noncod_merged.bed"
-        params.Faix_file = "$projectDir/data/zma_v4/zma_v4.fasta.fai"
-        params.Motif_tf_file = "$projectDir/data/zma_v4/zma_v4_motif_TF_file.txt"
-        params.Genes_coords = "$projectDir/data/zma_v4/zma_v4_genes_coords_sorted.bed"
-        params.Feature_file = "$projectDir/data/zma_v4/zma_v4_go_gene_file.txt"
-        params.TF_fam_file = "$projectDir/data/zma_v4/zma_v4_TF_family_file.txt"
-        params.Genes_metadata = "$projectDir/data/zma_v4/maize_v4_gene_metadata_file.txt"
-        params.P_val = 0.1
+    // define species id used for data subfolder and data file prefix
+    def species = "ath"
+    if(params.species == "maize_v4") {
+        species = "zma_v4"
+    } else if(params.species == "maize_v5") {
+        species = "zma_v5"
+    } else {
+        exit 1, "MINI-AC can only be run for the species 'arabidopsis', 'maize_v4' and 'maize_v5'. Instead it got '${params.species}'."
+    } 
+
+    // set input data parameters shared between genome-wide and locus-based modes
+    params.Faix_file = "$projectDir/data/${species}/${species}.fasta.fai"
+    params.Motif_tf_file = "$projectDir/data/${species}/${species}_motif_TF_file.txt"
+    params.Genes_coords = "$projectDir/data/${species}/${species}_genes_coords_sorted.bed"
+    params.Feature_file = "$projectDir/data/${species}/${species}_go_gene_file.txt"
+    params.TF_fam_file = "$projectDir/data/${species}/${species}_TF_family_file.txt"
+    params.Genes_metadata = "$projectDir/data/${species}/${species}_gene_metadata_file.txt"
+
+    // set defaut p-value
+    params.P_val = 0.1
+
+    if (params.mode == "genome_wide") {
         
-        genome_wide_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir, params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val, params.Bps_intersect, params.Second_gene_annot, params.Second_gene_dist, params.MotMapsFile_gw, params.Non_cod_genome, params.Faix_file, params.Motif_tf_file, params.Genes_coords, params.Feature_file, params.OBO_file, params.TF_fam_file, params.Genes_metadata)
-    }
-
-    else if (params.mode == "genome_wide" && params.species == "maize_v5") {
+        params.MotMapsFile_gw = "$projectDir/data/${species}/${species}_genome_wide_motif_mappings.bed"
+        params.Non_cod_genome = "$projectDir/data/${species}/${species}_noncod_merged.bed"
 
-        params.MotMapsFile_gw = "$projectDir/data/zma_v5/zma_v5_genome_wide_motif_mappings.bed"
-        params.Non_cod_genome = "$projectDir/data/zma_v5/zma_v5_noncod_merged.bed"
-        params.Faix_file = "$projectDir/data/zma_v5/zma_v5.fasta.fai"
-        params.Motif_tf_file = "$projectDir/data/zma_v5/zma_v5_motif_TF_file.txt"
-        params.Genes_coords = "$projectDir/data/zma_v5/zma_v5_genes_coords_sorted.bed"
-        params.Feature_file = "$projectDir/data/zma_v5/zma_v5_go_gene_file.txt"
-        params.TF_fam_file = "$projectDir/data/zma_v5/zma_v5_TF_family_file.txt"
-        params.Genes_metadata = "$projectDir/data/zma_v5/maize_v5_gene_metadata_file.txt"
-        params.P_val = 0.1
-        
         genome_wide_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir, params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val, params.Bps_intersect, params.Second_gene_annot, params.Second_gene_dist, params.MotMapsFile_gw, params.Non_cod_genome, params.Faix_file, params.Motif_tf_file, params.Genes_coords, params.Feature_file, params.OBO_file, params.TF_fam_file, params.Genes_metadata)
-    }
-
-    else if (params.mode == "genome_wide" && params.species == "arabidopsis") {
-
-        params.MotMapsFile_gw = "$projectDir/data/ath/ath_genome_wide_motif_mappings.bed"
-        params.Non_cod_genome = "$projectDir/data/ath/ath_noncod_merged.bed"
-        params.Faix_file = "$projectDir/data/ath/ath.fasta.fai"
-        params.Motif_tf_file = "$projectDir/data/ath/ath_motif_TF_file.txt"
-        params.Genes_coords = "$projectDir/data/ath/ath_genes_coords_sorted.bed"
-        params.Feature_file = "$projectDir/data/ath/ath_go_gene_file.txt"
-        params.TF_fam_file = "$projectDir/data/ath/ath_TF_family_file.txt"
-        params.Genes_metadata = "$projectDir/data/ath/arabidopsis_gene_metadata_file.txt"
-        params.P_val = 0.1
-
-        genome_wide_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir, params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val, params.Bps_intersect, params.Second_gene_annot, params.Second_gene_dist, params.MotMapsFile_gw, params.Non_cod_genome, params.Faix_file, params.Motif_tf_file, params.Genes_coords, params.Feature_file, params.OBO_file, params.TF_fam_file, params.Genes_metadata)
-
-    }
-
-    else if (params.mode == "locus_based" && params.species == "maize_v4") {
+    
+     else if (params.mode == "locus_based") {
 
-        params.MotMapsFile_lb = "$projectDir/data/zma_v4/zma_v4_locus_based_motif_mappings_5kbup_1kbdown.bed"
-        params.Promoter_file = "$projectDir/data/zma_v4/zma_v4_promoter_5kbup_1kbdown_sorted.bed"
-        params.Faix_file = "$projectDir/data/zma_v4/zma_v4.fasta.fai"
-        params.Motif_tf_file = "$projectDir/data/zma_v4/zma_v4_motif_TF_file.txt"
-        params.Feature_file = "$projectDir/data/zma_v4/zma_v4_go_gene_file.txt"
-        params.TF_fam_file = "$projectDir/data/zma_v4/zma_v4_TF_family_file.txt"
-        params.Genes_metadata = "$projectDir/data/zma_v4/maize_v4_gene_metadata_file.txt"
-        params.P_val = 0.01
+        params.MotMapsFile_lb = "$projectDir/data/${species}/${species}_locus_based_motif_mappings_5kbup_1kbdown.bed"
+        params.Promoter_file = "$projectDir/data/${species}/${species}_promoter_5kbup_1kbdown_sorted.bed"
         
         locus_based_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir, params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val, params.Bps_intersect, params.MotMapsFile_lb, params.Promoter_file, params.Faix_file, params.Motif_tf_file, params.Feature_file, params.OBO_file, params.TF_fam_file, params.Genes_metadata)
-
-    }
-
-    else if (params.mode == "locus_based" && params.species == "maize_v5") {
-
-        params.MotMapsFile_lb = "$projectDir/data/zma_v5/zma_v5_locus_based_motif_mappings_5kbup_1kbdown.bed"
-        params.Promoter_file = "$projectDir/data/zma_v5/zma_v5_promoter_5kbup_1kbdown_sorted.bed"
-        params.Faix_file = "$projectDir/data/zma_v5/zma_v5.fasta.fai"
-        params.Motif_tf_file = "$projectDir/data/zma_v5/zma_v5_motif_TF_file.txt"
-        params.Feature_file = "$projectDir/data/zma_v5/zma_v5_go_gene_file.txt"
-        params.TF_fam_file = "$projectDir/data/zma_v5/zma_v5_TF_family_file.txt"
-        params.Genes_metadata = "$projectDir/data/zma_v5/maize_v5_gene_metadata_file.txt"
-        params.P_val = 0.01
-        
-        locus_based_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir, params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val, params.Bps_intersect, params.MotMapsFile_lb, params.Promoter_file, params.Faix_file, params.Motif_tf_file, params.Feature_file, params.OBO_file, params.TF_fam_file, params.Genes_metadata)
-
+    
+    } else {
+        exit 1, "MINI-AC can only be run using the modes 'genome_wide' or 'locus_based'. Instead it got '${params.mode}'."
     }
-
-    else if (params.mode == "locus_based" && params.species == "arabidopsis") {
-
-        params.MotMapsFile_lb = "$projectDir/data/ath/ath_locus_based_motif_mappings_5kbup_1kbdown.bed"
-        params.Promoter_file = "$projectDir/data/ath/ath_promoter_5kbup_1kbdown_sorted.bed"
-        params.Faix_file = "$projectDir/data/ath/ath.fasta.fai"
-        params.Motif_tf_file = "$projectDir/data/ath/ath_motif_TF_file.txt"
-        params.Feature_file = "$projectDir/data/ath/ath_go_gene_file.txt"
-        params.TF_fam_file = "$projectDir/data/ath/ath_TF_family_file.txt"
-        params.Genes_metadata = "$projectDir/data/ath/arabidopsis_gene_metadata_file.txt"
-        params.P_val = 0.01
-
-        locus_based_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir, params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val, params.Bps_intersect, params.MotMapsFile_lb, params.Promoter_file, params.Faix_file, params.Motif_tf_file, params.Feature_file, params.OBO_file, params.TF_fam_file, params.Genes_metadata)
-    }
-
-    else {
-        exit 1, "MINI-AC can only be run using the modes 'genome_wide' and 'locus_based', and with the species 'arabidopsis', 'maize_v4' and 'maize_v5'. Instead it got '${params.species}' and '${params.mode}' "
-        }
 }
 
 

From a059ef2043b35dd2dbcd0712c26f769b6353ee5c Mon Sep 17 00:00:00 2001
From: Herman De Beukelaer <herman.debeukelaer@psb.ugent.be>
Date: Thu, 21 Sep 2023 12:06:33 +0200
Subject: [PATCH 03/15] Add missing curly brace

---
 mini_ac.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mini_ac.nf b/mini_ac.nf
index e4a2776..d8e792e 100755
--- a/mini_ac.nf
+++ b/mini_ac.nf
@@ -35,7 +35,7 @@ workflow MINIAC {
 
         genome_wide_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir, params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val, params.Bps_intersect, params.Second_gene_annot, params.Second_gene_dist, params.MotMapsFile_gw, params.Non_cod_genome, params.Faix_file, params.Motif_tf_file, params.Genes_coords, params.Feature_file, params.OBO_file, params.TF_fam_file, params.Genes_metadata)
     
-     else if (params.mode == "locus_based") {
+    } else if (params.mode == "locus_based") {
 
         params.MotMapsFile_lb = "$projectDir/data/${species}/${species}_locus_based_motif_mappings_5kbup_1kbdown.bed"
         params.Promoter_file = "$projectDir/data/${species}/${species}_promoter_5kbup_1kbdown_sorted.bed"

From 2c92d71c7f26efe9fe334e828bc32f38c7c4327d Mon Sep 17 00:00:00 2001
From: Herman De Beukelaer <herman.debeukelaer@psb.ugent.be>
Date: Thu, 21 Sep 2023 12:12:42 +0200
Subject: [PATCH 04/15] Use switch for setting species id

---
 mini_ac.nf | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/mini_ac.nf b/mini_ac.nf
index d8e792e..190f116 100755
--- a/mini_ac.nf
+++ b/mini_ac.nf
@@ -8,14 +8,17 @@ workflow MINIAC {
     params.OBO_file = "$projectDir/data/ontologies/go.obo"
 
     // define species id used for data subfolder and data file prefix
-    def species = "ath"
-    if(params.species == "maize_v4") {
-        species = "zma_v4"
-    } else if(params.species == "maize_v5") {
-        species = "zma_v5"
-    } else {
-        exit 1, "MINI-AC can only be run for the species 'arabidopsis', 'maize_v4' and 'maize_v5'. Instead it got '${params.species}'."
-    } 
+    def species
+    switch(params.species) {
+        case "arabidopsis":
+            species = "ath"
+        case "maize_v4":
+            species = "zma_v4"
+        case "maize_v5":
+            species = "zma_v5"
+        default:
+            exit 1, "MINI-AC can only be run for the species 'arabidopsis', 'maize_v4' and 'maize_v5'. Instead it got '${params.species}'."
+    }
 
     // set input data parameters shared between genome-wide and locus-based modes
     params.Faix_file = "$projectDir/data/${species}/${species}.fasta.fai"

From b52ec4656fe7fa4dd36c84e4ec9e666bbc35a73b Mon Sep 17 00:00:00 2001
From: Herman De Beukelaer <herman.debeukelaer@psb.ugent.be>
Date: Thu, 21 Sep 2023 12:20:59 +0200
Subject: [PATCH 05/15] Add missing breaks to switch

---
 mini_ac.nf | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/mini_ac.nf b/mini_ac.nf
index 190f116..1181637 100755
--- a/mini_ac.nf
+++ b/mini_ac.nf
@@ -12,10 +12,13 @@ workflow MINIAC {
     switch(params.species) {
         case "arabidopsis":
             species = "ath"
+            break
         case "maize_v4":
             species = "zma_v4"
+            break
         case "maize_v5":
             species = "zma_v5"
+            break
         default:
             exit 1, "MINI-AC can only be run for the species 'arabidopsis', 'maize_v4' and 'maize_v5'. Instead it got '${params.species}'."
     }

From 3138b1c5d1f03704400d3395f12df8744f48f1c2 Mon Sep 17 00:00:00 2001
From: Herman De Beukelaer <herman.debeukelaer@psb.ugent.be>
Date: Thu, 21 Sep 2023 12:24:18 +0200
Subject: [PATCH 06/15] Exclude nextflow cache dir and logs from version
 control

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..0d2264c
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,3 @@
+# ignore Nextflow cache and logs
+.nextflow/
+.nextflow.log*

From 9dfe14de2099ca80367f853694e092381dfafef1 Mon Sep 17 00:00:00 2001
From: Herman De Beukelaer <herman.debeukelaer@psb.ugent.be>
Date: Thu, 21 Sep 2023 14:16:33 +0200
Subject: [PATCH 07/15] Rename gene metadata files to match other file path
 structure

---
 ...bidopsis_gene_metadata_file.txt => ath_gene_metadata_file.txt} | 0
 ...ze_v4_gene_metadata_file.txt => zma_v4_gene_metadata_file.txt} | 0
 ...ze_v5_gene_metadata_file.txt => zma_v5_gene_metadata_file.txt} | 0
 3 files changed, 0 insertions(+), 0 deletions(-)
 rename data/ath/{arabidopsis_gene_metadata_file.txt => ath_gene_metadata_file.txt} (100%)
 rename data/zma_v4/{maize_v4_gene_metadata_file.txt => zma_v4_gene_metadata_file.txt} (100%)
 rename data/zma_v5/{maize_v5_gene_metadata_file.txt => zma_v5_gene_metadata_file.txt} (100%)

diff --git a/data/ath/arabidopsis_gene_metadata_file.txt b/data/ath/ath_gene_metadata_file.txt
similarity index 100%
rename from data/ath/arabidopsis_gene_metadata_file.txt
rename to data/ath/ath_gene_metadata_file.txt
diff --git a/data/zma_v4/maize_v4_gene_metadata_file.txt b/data/zma_v4/zma_v4_gene_metadata_file.txt
similarity index 100%
rename from data/zma_v4/maize_v4_gene_metadata_file.txt
rename to data/zma_v4/zma_v4_gene_metadata_file.txt
diff --git a/data/zma_v5/maize_v5_gene_metadata_file.txt b/data/zma_v5/zma_v5_gene_metadata_file.txt
similarity index 100%
rename from data/zma_v5/maize_v5_gene_metadata_file.txt
rename to data/zma_v5/zma_v5_gene_metadata_file.txt

From ddc800e282ed4f536a32c7b5ed10e4eb65426ed2 Mon Sep 17 00:00:00 2001
From: Herman De Beukelaer <herman.debeukelaer@psb.ugent.be>
Date: Thu, 21 Sep 2023 14:20:24 +0200
Subject: [PATCH 08/15] Rename MotMapsFile_gw and *_lb parameters to just
 MotifMapsFile

---
 docs/configuration_pipeline.md | 6 +++---
 mini_ac.nf                     | 8 ++++----
 workflows/miniac_gw.nf         | 4 ++--
 workflows/miniac_lb.nf         | 4 ++--
 4 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/docs/configuration_pipeline.md b/docs/configuration_pipeline.md
index d8668f9..4effad5 100644
--- a/docs/configuration_pipeline.md
+++ b/docs/configuration_pipeline.md
@@ -162,7 +162,7 @@ There are mainly two cases in which the user might want to alter the internal MI
 
 ### Modification of the motif mapping file for the locus-based mode of maize
 
-By default, the maize MINI-AC locus-based mode runs on the "medium" non-coding genomic space, which corresponds, for each locus in the genome, to the 5kb upstream of the translation start site, the 1kb downstream of the translation end site, and the introns. However, we generated two additional motif mapping files for the locus-based mode of maize, that cover "large" (15kb upstream of the translation start site, the 2.5kb downstream of the translation end site, and the introns), and "small" (1kb upstream of the translation start site, the 1kb downstream of the translation end site, and the introns) non-coding genomic spaces. For Arabidopsis only the "medium" non-coding genomic space motif mapping file was generated because it already covers 73.5% of the whole non-coding genomic psace (see publication). To use these files, first they need to be downloaded, and then, the corresponding parameters of the motif mapping file (```MotMapsFile_lb```) and the non-coding genomic space coordinates file (```Promoter_file```) should be modified either on the command line or in the configuration file.
+By default, the maize MINI-AC locus-based mode runs on the "medium" non-coding genomic space, which corresponds, for each locus in the genome, to the 5kb upstream of the translation start site, the 1kb downstream of the translation end site, and the introns. However, we generated two additional motif mapping files for the locus-based mode of maize, that cover "large" (15kb upstream of the translation start site, the 2.5kb downstream of the translation end site, and the introns), and "small" (1kb upstream of the translation start site, the 1kb downstream of the translation end site, and the introns) non-coding genomic spaces. For Arabidopsis only the "medium" non-coding genomic space motif mapping file was generated because it already covers 73.5% of the whole non-coding genomic psace (see publication). To use these files, first they need to be downloaded, and then, the corresponding parameters of the motif mapping file (```MotMapsFile```) and the non-coding genomic space coordinates file (```Promoter_file```) should be modified either on the command line or in the configuration file.
 
 To download the maize "large" motif mapping file and coordinates of the "large" non-coding genomic space:
 
@@ -180,14 +180,14 @@ wget https://zenodo.org/record/7974527/files/zma_promoter_1kbup_1kbdown_sorted.b
 Then (using the "small" definition as example), change the parameters on the command line:
 
 ```
-nextflow -C mini_ac.config run mini_ac.nf --mode locus_based --species maize --MotMapsFile_lb data/zma/zma_locus_based_motif_mappings_1kbup_1kbdown.bed --Promoter_file data/zma/zma_promoter_1kbup_1kbdown_sorted.bed
+nextflow -C mini_ac.config run mini_ac.nf --mode locus_based --species maize --MotMapsFile data/zma/zma_locus_based_motif_mappings_1kbup_1kbdown.bed --Promoter_file data/zma/zma_promoter_1kbup_1kbdown_sorted.bed
 ```
 or add them to the configuration file, along with the other parameters:
 
 ```nextflow
 params {
     /// [Other parameters...]
-    MotMapsFile_lb = "$projectDir/data/zma/zma_locus_based_motif_mappings_1kbup_1kbdown.bed"
+    MotMapsFile = "$projectDir/data/zma/zma_locus_based_motif_mappings_1kbup_1kbdown.bed"
     Promoter_file = "$projectDir/data/zma/zma_promoter_1kbup_1kbdown_sorted.bed"
     /// [Other parameters...]
 }
diff --git a/mini_ac.nf b/mini_ac.nf
index 1181637..fa26379 100755
--- a/mini_ac.nf
+++ b/mini_ac.nf
@@ -36,17 +36,17 @@ workflow MINIAC {
 
     if (params.mode == "genome_wide") {
         
-        params.MotMapsFile_gw = "$projectDir/data/${species}/${species}_genome_wide_motif_mappings.bed"
+        params.MotMapsFile = "$projectDir/data/${species}/${species}_genome_wide_motif_mappings.bed"
         params.Non_cod_genome = "$projectDir/data/${species}/${species}_noncod_merged.bed"
 
-        genome_wide_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir, params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val, params.Bps_intersect, params.Second_gene_annot, params.Second_gene_dist, params.MotMapsFile_gw, params.Non_cod_genome, params.Faix_file, params.Motif_tf_file, params.Genes_coords, params.Feature_file, params.OBO_file, params.TF_fam_file, params.Genes_metadata)
+        genome_wide_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir, params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val, params.Bps_intersect, params.Second_gene_annot, params.Second_gene_dist, params.MotMapsFile, params.Non_cod_genome, params.Faix_file, params.Motif_tf_file, params.Genes_coords, params.Feature_file, params.OBO_file, params.TF_fam_file, params.Genes_metadata)
     
     } else if (params.mode == "locus_based") {
 
-        params.MotMapsFile_lb = "$projectDir/data/${species}/${species}_locus_based_motif_mappings_5kbup_1kbdown.bed"
+        params.MotMapsFile = "$projectDir/data/${species}/${species}_locus_based_motif_mappings_5kbup_1kbdown.bed"
         params.Promoter_file = "$projectDir/data/${species}/${species}_promoter_5kbup_1kbdown_sorted.bed"
         
-        locus_based_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir, params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val, params.Bps_intersect, params.MotMapsFile_lb, params.Promoter_file, params.Faix_file, params.Motif_tf_file, params.Feature_file, params.OBO_file, params.TF_fam_file, params.Genes_metadata)
+        locus_based_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir, params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val, params.Bps_intersect, params.MotMapsFile, params.Promoter_file, params.Faix_file, params.Motif_tf_file, params.Feature_file, params.OBO_file, params.TF_fam_file, params.Genes_metadata)
     
     } else {
         exit 1, "MINI-AC can only be run using the modes 'genome_wide' or 'locus_based'. Instead it got '${params.mode}'."
diff --git a/workflows/miniac_gw.nf b/workflows/miniac_gw.nf
index 16c61bb..a45560d 100755
--- a/workflows/miniac_gw.nf
+++ b/workflows/miniac_gw.nf
@@ -274,7 +274,7 @@ workflow genome_wide_miniac {
     Bps_intersect
     Second_gene_annot
     Second_gene_dist
-    MotMapsFile_gw
+    MotMapsFile
     Non_cod_genome
     Faix_file
     Motif_tf_file
@@ -294,7 +294,7 @@ workflow genome_wide_miniac {
     parsed_acr = get_ACR_shufflings.out.acr_input
                                         .map {n -> [n.baseName.split("_")[0..-2].join("_"), n]}
 
-    motmaps_ch = Channel.fromPath(MotMapsFile_gw).ifEmpty { error "There was an error downloading the motif mapping files ${MotMapsFile_gw}" }
+    motmaps_ch = Channel.fromPath(MotMapsFile).ifEmpty { error "There was an error downloading the motif mapping files ${MotMapsFile}" }
 
     input_stats = acr_shufflings_ch.combine(motmaps_ch)
 
diff --git a/workflows/miniac_lb.nf b/workflows/miniac_lb.nf
index b5e1bd7..63be59e 100755
--- a/workflows/miniac_lb.nf
+++ b/workflows/miniac_lb.nf
@@ -273,7 +273,7 @@ workflow locus_based_miniac {
     One_DE_set
     P_val
     Bps_intersect
-    MotMapsFile_lb
+    MotMapsFile
     Promoter_file
     Faix_file
     Motif_tf_file
@@ -292,7 +292,7 @@ workflow locus_based_miniac {
     parsed_acr = get_ACR_shufflings.out.acr_input
                                         .map {n -> [n.baseName.split("_")[0..-2].join("_"), n]}
 
-    motmaps_ch = Channel.fromPath(MotMapsFile_lb).ifEmpty { error "There was an error downloading the motif mapping files ${MotMapsFile_lb}" }
+    motmaps_ch = Channel.fromPath(MotMapsFile).ifEmpty { error "There was an error downloading the motif mapping files ${MotMapsFile}" }
 
     input_stats = acr_shufflings_ch.combine(motmaps_ch)
 

From f8aa8cf7a345193cc36ec603869a1c4ae56e3714 Mon Sep 17 00:00:00 2001
From: Herman De Beukelaer <herman.debeukelaer@psb.ugent.be>
Date: Thu, 21 Sep 2023 14:37:08 +0200
Subject: [PATCH 09/15] Refine gitignore

---
 .gitignore | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.gitignore b/.gitignore
index 0d2264c..28f8d23 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,9 @@
 # ignore Nextflow cache and logs
 .nextflow/
 .nextflow.log*
+
+# ignore Singularity cache
+singularity_cache/
+
+# ignore large motif mapping files
+*motif_mappings*.bed

From b4149907d7b33698bf2680c43a72a9a1c0c95ae0 Mon Sep 17 00:00:00 2001
From: Herman De Beukelaer <herman.debeukelaer@psb.ugent.be>
Date: Thu, 21 Sep 2023 22:50:13 +0200
Subject: [PATCH 10/15] Ignore bin folder

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index 28f8d23..26ae0c2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,6 @@ singularity_cache/
 
 # ignore large motif mapping files
 *motif_mappings*.bed
+
+# ignore bin folder
+bin/
\ No newline at end of file

From b81569c2fcbb34ef8de6b2825221449a29288250 Mon Sep 17 00:00:00 2001
From: Herman De Beukelaer <herman.debeukelaer@psb.ugent.be>
Date: Thu, 28 Sep 2023 13:59:51 +0200
Subject: [PATCH 11/15] Revert accidental change of p-value for locus-based

---
 mini_ac.nf | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/mini_ac.nf b/mini_ac.nf
index 64cb1b4..935c2bb 100755
--- a/mini_ac.nf
+++ b/mini_ac.nf
@@ -34,14 +34,13 @@ workflow MINIAC {
     params.TF_fam_file = "$projectDir/data/${species}/${species}_TF_family_file.txt"
     params.Genes_metadata = "$projectDir/data/${species}/${species}_gene_metadata_file.txt"
 
-    // set defaut p-value
-    params.P_val = 0.1
-
     if (params.mode == "genome_wide") {
         
         params.MotMapsFile = "$projectDir/data/${species}/${species}_genome_wide_motif_mappings.bed"
         params.Non_cod_genome = "$projectDir/data/${species}/${species}_noncod_merged.bed"
 
+        params.P_val = 0.1
+
         genome_wide_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir,
             params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val,
             params.Bps_intersect, params.Second_gene_annot, params.Second_gene_dist, params.MotMapsFile,
@@ -53,6 +52,8 @@ workflow MINIAC {
 
         params.MotMapsFile = "$projectDir/data/${species}/${species}_locus_based_motif_mappings_5kbup_1kbdown.bed"
         params.Promoter_file = "$projectDir/data/${species}/${species}_promoter_5kbup_1kbdown_sorted.bed"
+
+        params.P_val = 0.01
         
         locus_based_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir,
             params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val,

From 99ea93bac3ce2364fd2e875f61fa556deb96ebfd Mon Sep 17 00:00:00 2001
From: Herman De Beukelaer <herman.debeukelaer@psb.ugent.be>
Date: Thu, 28 Sep 2023 14:34:01 +0200
Subject: [PATCH 12/15] Provide gene coords for gw mode only

---
 mini_ac.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mini_ac.nf b/mini_ac.nf
index 935c2bb..05dcfb3 100755
--- a/mini_ac.nf
+++ b/mini_ac.nf
@@ -29,7 +29,6 @@ workflow MINIAC {
     // set input data parameters shared between genome-wide and locus-based modes
     params.Faix_file = "$projectDir/data/${species}/${species}.fasta.fai"
     params.Motif_tf_file = "$projectDir/data/${species}/${species}_motif_TF_file.txt"
-    params.Genes_coords = "$projectDir/data/${species}/${species}_genes_coords_sorted.bed"
     params.Feature_file = "$projectDir/data/${species}/${species}_go_gene_file.txt"
     params.TF_fam_file = "$projectDir/data/${species}/${species}_TF_family_file.txt"
     params.Genes_metadata = "$projectDir/data/${species}/${species}_gene_metadata_file.txt"
@@ -38,6 +37,7 @@ workflow MINIAC {
         
         params.MotMapsFile = "$projectDir/data/${species}/${species}_genome_wide_motif_mappings.bed"
         params.Non_cod_genome = "$projectDir/data/${species}/${species}_noncod_merged.bed"
+        params.Genes_coords = "$projectDir/data/${species}/${species}_genes_coords_sorted.bed"
 
         params.P_val = 0.1
 

From b5637eea393ef7038557525f237993879460a39c Mon Sep 17 00:00:00 2001
From: Herman De Beukelaer <herman.debeukelaer@psb.ugent.be>
Date: Thu, 28 Sep 2023 14:34:19 +0200
Subject: [PATCH 13/15] Correct test input file paths due to rename

---
 tests/mini_ac.nf.test | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/mini_ac.nf.test b/tests/mini_ac.nf.test
index 5eb172e..2fd20b2 100644
--- a/tests/mini_ac.nf.test
+++ b/tests/mini_ac.nf.test
@@ -29,7 +29,7 @@ nextflow_workflow {
                 Genes_coords = "${baseDir}/data/zma_v4/zma_v4_genes_coords_sorted.bed"
                 Feature_file = "${baseDir}/data/zma_v4/zma_v4_go_gene_file.txt"
                 TF_fam_file = "${baseDir}/data/zma_v4/zma_v4_TF_family_file.txt"
-                Genes_metadata = "${baseDir}/data/zma_v4/maize_v4_gene_metadata_file.txt"
+                Genes_metadata = "${baseDir}/data/zma_v4/zma_v4_gene_metadata_file.txt"
                 OBO_file = "${baseDir}/data/ontologies/go.obo"
 
                 //// Output folder
@@ -103,7 +103,7 @@ nextflow_workflow {
                 Motif_tf_file = "${baseDir}/data/zma_v4/zma_v4_motif_TF_file.txt"
                 Feature_file = "${baseDir}/data/zma_v4/zma_v4_go_gene_file.txt"
                 TF_fam_file = "${baseDir}/data/zma_v4/zma_v4_TF_family_file.txt"
-                Genes_metadata = "${baseDir}/data/zma_v4/maize_v4_gene_metadata_file.txt"
+                Genes_metadata = "${baseDir}/data/zma_v4/zma_v4_gene_metadata_file.txt"
                 OBO_file = "${baseDir}/data/ontologies/go.obo"
 
                 //// Output folder
@@ -172,7 +172,7 @@ nextflow_workflow {
                 Genes_coords = "${baseDir}/data/ath/ath_genes_coords_sorted.bed"
                 Feature_file = "${baseDir}/data/ath/ath_go_gene_file.txt"
                 TF_fam_file = "${baseDir}/data/ath/ath_TF_family_file.txt"
-                Genes_metadata = "${baseDir}/data/ath/arabidopsis_gene_metadata_file.txt"
+                Genes_metadata = "${baseDir}/data/ath/ath_gene_metadata_file.txt"
                 OBO_file = "${baseDir}/data/ontologies/go.obo"
 
                 //// Output folder
@@ -244,7 +244,7 @@ nextflow_workflow {
                 Motif_tf_file = "${baseDir}/data/ath/ath_motif_TF_file.txt"
                 Feature_file = "${baseDir}/data/ath/ath_go_gene_file.txt"
                 TF_fam_file = "${baseDir}/data/ath/ath_TF_family_file.txt"
-                Genes_metadata = "${baseDir}/data/ath/arabidopsis_gene_metadata_file.txt"
+                Genes_metadata = "${baseDir}/data/ath/ath_gene_metadata_file.txt"
                 OBO_file = "${baseDir}/data/ontologies/go.obo"
 
                 //// Output folder

From d70ee8dabf081f3ad08b6a1ece414472655a1999 Mon Sep 17 00:00:00 2001
From: Herman De Beukelaer <herman.debeukelaer@psb.ugent.be>
Date: Thu, 28 Sep 2023 16:18:30 +0200
Subject: [PATCH 14/15] Pass full params object from main workflow to gw and lb
 workflows

---
 mini_ac.nf             | 13 ++------
 workflows/miniac_gw.nf | 70 +++++++++++++++---------------------------
 workflows/miniac_lb.nf | 67 ++++++++++++++--------------------------
 3 files changed, 49 insertions(+), 101 deletions(-)

diff --git a/mini_ac.nf b/mini_ac.nf
index 05dcfb3..4f81ca6 100755
--- a/mini_ac.nf
+++ b/mini_ac.nf
@@ -41,12 +41,7 @@ workflow MINIAC {
 
         params.P_val = 0.1
 
-        genome_wide_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir,
-            params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val,
-            params.Bps_intersect, params.Second_gene_annot, params.Second_gene_dist, params.MotMapsFile,
-            params.Non_cod_genome, params.Faix_file, params.Motif_tf_file, params.Genes_coords, params.Feature_file,
-            params.OBO_file, params.TF_fam_file, params.Genes_metadata, params.Shuffle_count, params.Shuffle_seed,
-            params.Csv_output)
+        genome_wide_miniac(params)
     
     } else if (params.mode == "locus_based") {
 
@@ -55,11 +50,7 @@ workflow MINIAC {
 
         params.P_val = 0.01
         
-        locus_based_miniac(params.OutDir, params.ACR_dir, params.Filter_set_genes, params.Set_genes_dir,
-            params.One_filtering_set, params.DE_genes, params.DE_genes_dir, params.One_DE_set, params.P_val,
-            params.Bps_intersect, params.MotMapsFile, params.Promoter_file, params.Faix_file, params.Motif_tf_file,
-            params.Feature_file, params.OBO_file, params.TF_fam_file, params.Genes_metadata, params.Shuffle_count,
-            params.Shuffle_seed, params.Csv_output)
+        locus_based_miniac(params)
     
     } else {
         exit 1, "MINI-AC can only be run using the modes 'genome_wide' or 'locus_based'. Instead it got '${params.mode}'."
diff --git a/workflows/miniac_gw.nf b/workflows/miniac_gw.nf
index c079b7f..fe5e551 100755
--- a/workflows/miniac_gw.nf
+++ b/workflows/miniac_gw.nf
@@ -268,53 +268,30 @@ process getIntegrativeOutputs {
 
 workflow genome_wide_miniac {
     take:
-    OutDir
-    ACR_dir
-    Filter_set_genes
-    Set_genes_dir
-    One_filtering_set
-    DE_genes
-    DE_genes_dir
-    One_DE_set
-    P_val
-    Bps_intersect
-    Second_gene_annot
-    Second_gene_dist
-    MotMapsFile
-    Non_cod_genome
-    Faix_file
-    Motif_tf_file
-    Genes_coords
-    Feature_file
-    OBO_file
-    TF_fam_file
-    Genes_metadata
-    Shuffle_count
-    Shuffle_seed
-    Csv_output
+    params
 
     main:
     
-    if (!file(MotMapsFile).exists()) { error "Please make sure that you downloaded the motif mapping files as described in the documentation." }
+    if (!file(params.MotMapsFile).exists()) { error "Please make sure that you downloaded the motif mapping files as described in the documentation." }
     
-    ACR_files = Channel.fromPath("${ACR_dir}/*.bed").ifEmpty { error "No *.bed files could be found in the specified ACR directory ${ACR_dir}" }
+    ACR_files = Channel.fromPath("${params.ACR_dir}/*.bed").ifEmpty { error "No *.bed files could be found in the specified ACR directory ${params.ACR_dir}" }
     
-    get_ACR_shufflings(ACR_files, Faix_file, Non_cod_genome, Shuffle_count, Shuffle_seed)    
+    get_ACR_shufflings(ACR_files, params.Faix_file, params.Non_cod_genome, params.Shuffle_count, params.Shuffle_seed)    
 
     acr_shufflings_ch = get_ACR_shufflings.out.shufflings
 
     parsed_acr = get_ACR_shufflings.out.acr_input
                                         .map {n -> [n.baseName.split("_")[0..-2].join("_"), n]}
 
-    motmaps_ch = Channel.fromPath(MotMapsFile)
+    motmaps_ch = Channel.fromPath(params.MotMapsFile)
 
     input_stats = acr_shufflings_ch.combine(motmaps_ch)
 
-    if (Bps_intersect == false) {
+    if (params.Bps_intersect == false) {
 
         script_proc_stats = "${projectDir}/bin/processStats_gw.py"
 
-        getStats(input_stats, script_proc_stats, Motif_tf_file, OutDir, Shuffle_count)
+        getStats(input_stats, script_proc_stats, params.Motif_tf_file, params.OutDir, params.Shuffle_count)
 
         stats_ch = getStats.out.proc_stats
                     .map { n -> [n.BaseName.split("_")[0..-5].join("_"), n]}
@@ -325,7 +302,7 @@ workflow genome_wide_miniac {
         
         script_proc_stats_bps = "${projectDir}/bin/processStats_bps_gw.py"
 
-        getStats_bps(input_stats, script_proc_stats_bps, Motif_tf_file, OutDir, Shuffle_count)
+        getStats_bps(input_stats, script_proc_stats_bps, params.Motif_tf_file, params.OutDir, params.Shuffle_count)
 
         stats_ch = getStats_bps.out.proc_stats
                     .map { n -> [n.BaseName.split("_")[0..-5].join("_"), n]}
@@ -337,18 +314,19 @@ workflow genome_wide_miniac {
 
     script_getnetwork = "${projectDir}/bin/getNetwork_gw.py"
 
-    getNetwork(stats_acr_motmaps_ch, Genes_coords, script_getnetwork, Motif_tf_file, Second_gene_dist, Second_gene_annot, P_val, OutDir)
+    getNetwork(stats_acr_motmaps_ch, params.Genes_coords, script_getnetwork, params.Motif_tf_file,
+               params.Second_gene_dist, params.Second_gene_annot, params.P_val, params.OutDir)
 
     networks = getNetwork.out
 
-    if (Filter_set_genes == true) {
+    if (params.Filter_set_genes == true) {
 
         filteringScript = "${projectDir}/bin/filterNetwork_gw.py"
 
-        filt_set_files = Channel.fromPath("${Set_genes_dir}/*.txt")
-                .ifEmpty { error "Cannot find any directory: ${Set_genes_dir}" }
+        filt_set_files = Channel.fromPath("${params.Set_genes_dir}/*.txt")
+                .ifEmpty { error "Cannot find any directory: ${params.Set_genes_dir}" }
 
-        if (One_filtering_set == true) {
+        if (params.One_filtering_set == true) {
 
             networks_gene_set = networks.combine(filt_set_files)
 
@@ -373,7 +351,7 @@ workflow genome_wide_miniac {
 
                                             }
 
-        filterSetOfGenes(filteringScript, networks_gene_set, OutDir)
+        filterSetOfGenes(filteringScript, networks_gene_set, params.OutDir)
 
         net_tuple = filterSetOfGenes.out
                     .map { n -> [n.BaseName.split("_")[0..-3].join("_"), n]}
@@ -395,21 +373,20 @@ workflow genome_wide_miniac {
     script_add_go_names = "${projectDir}/bin/add_go_names.py"
     script_filter_reduced = "${projectDir}/bin/FilterReduceGO.py"
 
-    GOenrichment(net_tuple, Feature_file,
-                script_enricher, script_reduce_go,
-                script_add_go_names, OBO_file, script_filter_reduced, OutDir)
+    GOenrichment(net_tuple, params.Feature_file, script_enricher, script_reduce_go,
+                script_add_go_names, params.OBO_file, script_filter_reduced, params.OutDir)
 
     go_tuple = GOenrichment.out
             .map { n -> [n.BaseName.split("_")[0..-3].join("_"), n]}
 
     int_input = int_input.join(go_tuple)
 
-    if (DE_genes == true) {
+    if (params.DE_genes == true) {
 
-        de_files = Channel.fromPath("${DE_genes_dir}/*.txt")
-                                .ifEmpty { error "Cannot find any directory: ${Set_genes_dir}" }
+        de_files = Channel.fromPath("${params.DE_genes_dir}/*.txt")
+                                .ifEmpty { error "Cannot find any directory: ${params.Set_genes_dir}" }
 
-        if (One_DE_set == true) {
+        if (params.One_DE_set == true) {
 
             int_input = int_input.combine(de_files)
 
@@ -435,7 +412,8 @@ workflow genome_wide_miniac {
     script_go_file = "${projectDir}/bin/getGO_xlsx_gw.py"
     script_net_files = "${projectDir}/bin/getNetVisualizationOutput_gw.py"
 
-    getIntegrativeOutputs(int_input, Motif_tf_file, TF_fam_file, Genes_metadata, P_val, Filter_set_genes, DE_genes,
-                          script_tf_file, script_motif_file, script_go_file, script_net_files, OutDir, Csv_output)
+    getIntegrativeOutputs(int_input, params.Motif_tf_file, params.TF_fam_file, params.Genes_metadata, params.P_val,
+                          params.Filter_set_genes, params.DE_genes, script_tf_file, script_motif_file, script_go_file,
+                          script_net_files, params.OutDir, params.Csv_output)
 
         }
diff --git a/workflows/miniac_lb.nf b/workflows/miniac_lb.nf
index 15c3848..e84fd43 100755
--- a/workflows/miniac_lb.nf
+++ b/workflows/miniac_lb.nf
@@ -267,52 +267,31 @@ process getIntegrativeOutputs {
 }
 
 workflow locus_based_miniac {
-
     take:
-    OutDir
-    ACR_dir
-    Filter_set_genes
-    Set_genes_dir
-    One_filtering_set
-    DE_genes
-    DE_genes_dir
-    One_DE_set
-    P_val
-    Bps_intersect
-    MotMapsFile
-    Promoter_file
-    Faix_file
-    Motif_tf_file
-    Feature_file
-    OBO_file
-    TF_fam_file
-    Genes_metadata
-    Shuffle_count
-    Shuffle_seed
-    Csv_output
+    params
 
     main:
 
-    if (!file(MotMapsFile).exists()) { error "Please make sure that you downloaded the motif mapping files as described in the documentation." }
+    if (!file(params.MotMapsFile).exists()) { error "Please make sure that you downloaded the motif mapping files as described in the documentation." }
 
-    ACR_files = Channel.fromPath("${ACR_dir}/*.bed").ifEmpty { error "No *.bed files could be found in the specified ACR directory ${ACR_dir}" }
+    ACR_files = Channel.fromPath("${params.ACR_dir}/*.bed").ifEmpty { error "No *.bed files could be found in the specified ACR directory ${params.ACR_dir}" }
     
-    get_ACR_shufflings(ACR_files, Faix_file, Promoter_file, Shuffle_count, Shuffle_seed)    
+    get_ACR_shufflings(ACR_files, params.Faix_file, params.Promoter_file, params.Shuffle_count, params.Shuffle_seed)    
 
     acr_shufflings_ch = get_ACR_shufflings.out.shufflings
 
     parsed_acr = get_ACR_shufflings.out.acr_input
                                         .map {n -> [n.baseName.split("_")[0..-2].join("_"), n]}
 
-    motmaps_ch = Channel.fromPath(MotMapsFile)
+    motmaps_ch = Channel.fromPath(params.MotMapsFile)
 
     input_stats = acr_shufflings_ch.combine(motmaps_ch)
 
-    if (Bps_intersect == false) {
+    if (params.Bps_intersect == false) {
 
         script_proc_stats = "${projectDir}/bin/processStats_lb.py"
 
-        getStats(input_stats, script_proc_stats, Motif_tf_file, Promoter_file, OutDir, Shuffle_count)
+        getStats(input_stats, script_proc_stats, params.Motif_tf_file, params.Promoter_file, params.OutDir, params.Shuffle_count)
 
         stats_ch = getStats.out.proc_stats
                     .map { n -> [n.BaseName.split("_")[0..-5].join("_"), n]}
@@ -322,7 +301,7 @@ workflow locus_based_miniac {
         
         script_proc_stats_bps = "${projectDir}/bin/processStats_bps_lb.py"
 
-        getStats_bps(input_stats, script_proc_stats_bps, Motif_tf_file, Promoter_file, OutDir, Shuffle_count)
+        getStats_bps(input_stats, script_proc_stats_bps, params.Motif_tf_file, params.Promoter_file, params.OutDir, params.Shuffle_count)
 
         stats_ch = getStats_bps.out.proc_stats
                     .map { n -> [n.BaseName.split("_")[0..-5].join("_"), n]}
@@ -334,18 +313,18 @@ workflow locus_based_miniac {
 
     script_getnetwork = "${projectDir}/bin/getNetwork_lb.py"
 
-    getNetwork(stats_acr_motmaps_ch, Promoter_file, script_getnetwork, Motif_tf_file, P_val, OutDir)
+    getNetwork(stats_acr_motmaps_ch, params.Promoter_file, script_getnetwork, params.Motif_tf_file, params.P_val, params.OutDir)
 
     networks = getNetwork.out
 
-    if (Filter_set_genes == true) {
+    if (params.Filter_set_genes == true) {
 
         filteringScript = "${projectDir}/bin/filterNetwork_lb.py"
 
-        filt_set_files = Channel.fromPath("${Set_genes_dir}/*.txt")
-                .ifEmpty { error "Cannot find any directory: ${Set_genes_dir}" }
+        filt_set_files = Channel.fromPath("${params.Set_genes_dir}/*.txt")
+                .ifEmpty { error "Cannot find any directory: ${params.Set_genes_dir}" }
 
-        if (One_filtering_set == true) {
+        if (params.One_filtering_set == true) {
 
             networks_gene_set = networks.combine(filt_set_files)
 
@@ -370,7 +349,7 @@ workflow locus_based_miniac {
 
                                             }
 
-        filterSetOfGenes(filteringScript, networks_gene_set, OutDir)
+        filterSetOfGenes(filteringScript, networks_gene_set, params.OutDir)
 
         net_tuple = filterSetOfGenes.out
                     .map { n -> [n.BaseName.split("_")[0..-3].join("_"), n]}
@@ -393,21 +372,20 @@ workflow locus_based_miniac {
     script_filter_reduced = "${projectDir}/bin/FilterReduceGO.py"
 
 
-    GOenrichment(net_tuple, Feature_file,
-                script_enricher, script_reduce_go,
-                script_add_go_names, OBO_file, script_filter_reduced, OutDir)
+    GOenrichment(net_tuple, params.Feature_file, script_enricher, script_reduce_go,
+                script_add_go_names, params.OBO_file, script_filter_reduced, params.OutDir)
 
     go_tuple = GOenrichment.out
             .map { n -> [n.BaseName.split("_")[0..-3].join("_"), n]}
 
     int_input = int_input.join(go_tuple)
 
-    if (DE_genes == true) {
+    if (params.DE_genes == true) {
 
-        de_files = Channel.fromPath("${DE_genes_dir}/*.txt")
-                                .ifEmpty { error "Cannot find any directory: ${Set_genes_dir}" }
+        de_files = Channel.fromPath("${params.DE_genes_dir}/*.txt")
+                                .ifEmpty { error "Cannot find any directory: ${params.Set_genes_dir}" }
 
-        if (One_DE_set == true) {
+        if (params.One_DE_set == true) {
 
             int_input = int_input.combine(de_files)
 
@@ -433,7 +411,8 @@ workflow locus_based_miniac {
     script_go_file = "${projectDir}/bin/getGO_xlsx_lb.py"
     script_net_files = "${projectDir}/bin/getNetVisualizationOutput_lb.py"
 
-    getIntegrativeOutputs(int_input, Motif_tf_file, TF_fam_file, Genes_metadata, P_val, Filter_set_genes, DE_genes,
-                          script_tf_file, script_motif_file, script_go_file, script_net_files, OutDir, Csv_output)
+    getIntegrativeOutputs(int_input, params.Motif_tf_file, params.TF_fam_file, params.Genes_metadata, params.P_val,
+                          params.Filter_set_genes, params.DE_genes, script_tf_file, script_motif_file, script_go_file,
+                          script_net_files, params.OutDir, params.Csv_output)
 
 }

From bef0d0769411f5c2bac047a43b52f3ee3a55f66d Mon Sep 17 00:00:00 2001
From: Nicolas MANOSALVA PEREZ <niman@psb.ugent.be>
Date: Fri, 29 Sep 2023 09:53:34 +0200
Subject: [PATCH 15/15] update on .gitignore

---
 .gitignore | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.gitignore b/.gitignore
index c612040..573806b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,3 +20,10 @@ tests/outputs/
 # ignore SLURM output and error files
 slurm.*.out
 slurm.*.err
+
+# ignore jupyter notebook checkpoints
+.ipynb_checkpoints/
+
+# python cache and compiled files
+__pycache__/
+*.pyc
\ No newline at end of file