Fix --res_zoomify (#229)

.nf-core.yml

@@ -10,4 +10,4 @@ template:
   name: hic
   org: nf-core
   outdir: .
-  version: 2.2.0dev
+  version: 2.2.0

.vscode/settings.json

@@ -1,3 +1,4 @@
 {
-    "markdown.styles": ["public/vscode_markdown.css"]
+    "markdown.styles": ["public/vscode_markdown.css"],
+    "nextflow.telemetry.enabled": false
 }

CHANGELOG.md

@@ -3,14 +3,53 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Version 2.2.0 2026-03-02
+
+### `Added`
+
+- Subworkflows meta.yml
+- Module FAIDX for chromosomes sizes calculation
+- TRIMGALORE module for 5' clipping (see #225)
+- CALDER2 compartments calling (see '--compartments_caller' option)
+- Local FILTER_CHROMSIZE module (in order to apply CALDER2 without error)
+- Optional '--min_size' parameter for chromosome selection
+- Default MIN_FRAG_SIZE, MAX_FRAG_SIZE, MIN_INSERT_SIZE and MAX_INSERT_SIZE values for Arima and ArimV2 protocols
+
+### `Removed`
+
+- Module GETCHROMSIZES (replaced by FAIDX)
+- Version channels from subworkflows (tools versions gathering still a WIP)
+
+### `Fixed`
+
+- #227: MPLCONFIGDIR is set to "${baseDir}/mplconfig"
+- #62: a single number can be given as BIN_SIZES without error
+- #225:TRIMGALORE remove the first 5 bases of the 5' end and
+  fragments and inserts size min/max settings are set to recommended values if Arima/ArimaV2 is used
+- Bug from COOLER_CLOAD deprecated "pairs" ext.args calling
+- Bug on the cooler "add resolution" step caused by module COOLER_CLOAD update
+- Logo matching template
+
+### `Updated`
+
+- All nf-core modules (including topics channel)
+- Modules path
+- "channel" syntax with lowercase c
+- Components names in subworkflows meta.yml
+- COOLER_CLOAD inputs and outputs
+- BWA_MEM inputs
+- SAMTOOL_SORT inputs
+- UTILS_NFSCHEMA_PLUGIN inputs and outputs
+- Markdown settings
+- Template files
+- nf-core version to 3.5.0
+
 ## v2.2.0dev
 
 ### `Added`
 
 - Parameter `--dnase`is now replaced by `--no_digestion`
 
-- Add CALDER2 compartments calling (see '--compartments_caller' option)
-
 - Add new '--balancing_opts' to update `cooler balance` arguments (#193)
 
 - New subworkflow based on `pairtools` to detect valid pairs. The user

conf/modules.config

@@ -10,6 +10,10 @@ process {
         ext.args = '--quiet'
     }
 
+    withName: TRIMGALORE {
+        ext.args = '--clip_R1 5 --clip_R2 5'
+    }
+
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
@@ -37,14 +41,6 @@ process {
         ]
     }
 
-    withName: 'CUSTOM_GETCHROMSIZES' {
-        publishDir = [
-            path: { "${params.outdir}/genome" },
-            mode: 'copy',
-            enabled: params.save_reference
-        ]
-    }
-
     withName: 'GET_RESTRICTION_FRAGMENTS' {
         publishDir = [
             path: { "${params.outdir}/genome" },
@@ -344,7 +340,7 @@ process {
             enabled : params.save_raw_maps
         ]
         ext.prefix = { "${meta.id}.${cool_bin}" }
-        ext.args = "pairs -c1 2 -p1 3 -c2 4 -p2 5"
+        ext.args = "-c1 2 -p1 3 -c2 4 -p2 5"
     }
 
     withName: 'COOLER_BALANCE' {

main.nf

@@ -47,8 +47,6 @@ workflow NFCORE_HIC {
 
     main:
 
-    ch_versions = Channel.empty()
-
     //
     // SUBWORKFLOW: prepare genome annotation
     //
@@ -57,7 +55,6 @@ workflow NFCORE_HIC {
         params.bwt2_index,
         params.bwa_index
     )
-    ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
 
     //
     // WORKFLOW: Run pipeline

modules.json

@@ -7,122 +7,127 @@
                 "nf-core": {
                     "bowtie2/align": {
                         "branch": "master",
-                        "git_sha": "e4bad511789f16d0df39ee306b2cd50418365048",
+                        "git_sha": "ab146e7909edbf6dcc6459de57eef29dceb61d42",
                         "installed_by": ["modules"]
                     },
                     "bowtie2/build": {
                         "branch": "master",
-                        "git_sha": "1fea64f5132a813ec97c1c6d3a74e0aee7142b6d",
+                        "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf",
                         "installed_by": ["modules"]
                     },
                     "bwa/index": {
                         "branch": "master",
-                        "git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b",
+                        "git_sha": "966ba9887e2b04d89d64db06c01508873bde13b1",
                         "installed_by": ["modules"]
                     },
                     "bwa/mem": {
                         "branch": "master",
-                        "git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b",
+                        "git_sha": "707241c72951f24fd89982c4c80c5983a4c437ef",
                         "installed_by": ["modules"]
                     },
                     "calder2": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "cooler/balance": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "5d491ae33d61ab37e13850951b92ae7d6e3f4e31",
                         "installed_by": ["modules"]
                     },
                     "cooler/cload": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "5d491ae33d61ab37e13850951b92ae7d6e3f4e31",
                         "installed_by": ["modules"]
                     },
                     "cooler/dump": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "5d491ae33d61ab37e13850951b92ae7d6e3f4e31",
                         "installed_by": ["modules"]
                     },
                     "cooler/makebins": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "5d491ae33d61ab37e13850951b92ae7d6e3f4e31",
                         "installed_by": ["modules"]
                     },
                     "cooler/zoomify": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
-                    },
-                    "custom/getchromsizes": {
-                        "branch": "master",
-                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "git_sha": "5d491ae33d61ab37e13850951b92ae7d6e3f4e31",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
+                        "git_sha": "2c73cc8fa92cf48de3da0b643fdf357a8a290b36",
                         "installed_by": ["modules"]
                     },
                     "pairix": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "pairtools/dedup": {
                         "branch": "master",
-                        "git_sha": "4d3743f71f43cc40505dee2bc0747dca2df5f69a",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "pairtools/merge": {
                         "branch": "master",
-                        "git_sha": "4d3743f71f43cc40505dee2bc0747dca2df5f69a",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "pairtools/parse": {
                         "branch": "master",
-                        "git_sha": "4d3743f71f43cc40505dee2bc0747dca2df5f69a",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "pairtools/restrict": {
                         "branch": "master",
-                        "git_sha": "4d3743f71f43cc40505dee2bc0747dca2df5f69a",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
                     "pairtools/select": {
                         "branch": "master",
-                        "git_sha": "4d3743f71f43cc40505dee2bc0747dca2df5f69a",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "pairtools/sort": {
                         "branch": "master",
-                        "git_sha": "4d3743f71f43cc40505dee2bc0747dca2df5f69a",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "pairtools/stats": {
                         "branch": "master",
-                        "git_sha": "4d3743f71f43cc40505dee2bc0747dca2df5f69a",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "installed_by": ["modules"]
+                    },
+                    "samtools/faidx": {
+                        "branch": "master",
+                        "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
                         "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7",
+                        "installed_by": ["modules"]
+                    },
+                    "trimgalore": {
+                        "branch": "master",
+                        "git_sha": "eed5d14302a6c9070dcc25feeab707a27a4b3254",
                         "installed_by": ["modules"]
                     }
                 }
@@ -141,7 +146,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
+                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
                         "installed_by": ["subworkflows"]
                     }
                 }

modules/local/filter_chromsize/main.nf

@@ -0,0 +1,20 @@
+/*
+ * Filter chromsize
+ * Filter out chromosomes smaller than a given threshold
+ */
+
+process FILTER_CHROMSIZE {
+    tag "${meta.id}"
+    label 'process_low'
+
+    input:
+    tuple val(meta), path(sizes_file)
+
+    output:
+    tuple val(meta), path("filtered.sizes")
+
+    script:
+    """
+    awk -v MIN=${params.min_size} '\$2 >= MIN' ${sizes_file} > filtered.sizes
+    """
+}