diff --git a/modules/local/filterbam/main.nf b/modules/local/filterbam/main.nf
index 0f63be60330d928711dff04923ea7e3d562e5b76..525c49ad5d52a99c7926110508c8d97c5736ec7f 100644
--- a/modules/local/filterbam/main.nf
+++ b/modules/local/filterbam/main.nf
@@ -5,7 +5,7 @@ process FILTER_PAIR {
conda "bioconda::samtools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
- 'quay.io/biocontainers/samtools:1.17--h00cdaf9_0' }"
+ 'biocontainers/samtools:1.17--h00cdaf9_0' }"
input:
tuple val(meta1), path(bam1), val(meta2), path(bam2)
@@ -22,4 +22,4 @@ process FILTER_PAIR {
samtools view -h -N common_reads.txt ${bam2} -O BAM > ${meta2.id}_2paired.bam
"""
-}
\ No newline at end of file
+}
diff --git a/modules/local/hicexplorer/hicPlotMatrix.nf b/modules/local/hicexplorer/hicPlotMatrix.nf
index 8041aa1e3afe88acb2cc3ac26c9ce25b10d45d0a..60e1fecb1fc0995abccb5438086766b404823af0 100644
--- a/modules/local/hicexplorer/hicPlotMatrix.nf
+++ b/modules/local/hicexplorer/hicPlotMatrix.nf
@@ -5,7 +5,7 @@ process HIC_PLOT_MATRIX {
conda "bioconda::hicexplorer=3.7.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
- 'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
+ 'biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
input:
diff --git a/modules/local/hicstuff/bam2pairs.nf b/modules/local/hicstuff/bam2pairs.nf
index 4b2b26ecccceba423ef20270116a433650803ac5..fba720deb96aae3446c3c4fb78ed524b28bea477 100644
--- a/modules/local/hicstuff/bam2pairs.nf
+++ b/modules/local/hicstuff/bam2pairs.nf
@@ -3,7 +3,7 @@ process BAM2PAIRS {
label 'process_high'
conda "conda-forge::python=3.9 conda-forge::biopython=1.80 conda-forge::numpy=1.22.3 conda-forge::matplotlib=3.6.3 conda-forge::pandas=1.5.3"
- container = "lbmc/hicstuff:3.1.3"
+ container = "docker.io/lbmc/hicstuff:3.1.3"
input:
tuple val(meta1), path(bam1), val(meta2), path(bam2)
diff --git a/modules/local/hicstuff/build_matrix.nf b/modules/local/hicstuff/build_matrix.nf
index d8ff6a6a21726028d4d1ff35fb282382f0e7864e..4d531e94bc82cebc697fbae63730aac58608fc79 100644
--- a/modules/local/hicstuff/build_matrix.nf
+++ b/modules/local/hicstuff/build_matrix.nf
@@ -3,7 +3,7 @@ process BUILD_MATRIX {
label 'process_single'
conda "conda-forge::python=3.9 conda-forge::biopython=1.80 conda-forge::numpy=1.22.3 conda-forge::matplotlib=3.6.3 conda-forge::pandas=1.5.3"
- container = "lbmc/hicstuff:3.1.3"
+ container = "docker.io/lbmc/hicstuff:3.1.3"
input:
tuple val(meta1), path(idx_pairs)
diff --git a/modules/local/hicstuff/build_matrix_cool.nf b/modules/local/hicstuff/build_matrix_cool.nf
index 36110614ecb9f0e1014cdf19904fe56d5f83ad0e..b39f66901425ce46e88b64a702790f04acb992cb 100644
--- a/modules/local/hicstuff/build_matrix_cool.nf
+++ b/modules/local/hicstuff/build_matrix_cool.nf
@@ -3,7 +3,7 @@ process BUILD_MATRIX_COOL {
label 'process_single'
conda "conda-forge::python=3.9 conda-forge::biopython=1.80 conda-forge::numpy=1.22.3 conda-forge::matplotlib=3.6.3 conda-forge::pandas=1.5.3"
- container = "lbmc/hicstuff:3.1.3"
+ container = "docker.io/lbmc/hicstuff:3.1.3"
input:
tuple val(meta1), path(idx_pairs)
diff --git a/modules/local/hicstuff/build_matrix_cool_alt.nf b/modules/local/hicstuff/build_matrix_cool_alt.nf
index a52465dcbc9f76e6d4249f74d9da44ea2d810de1..93dfd3512642cd6597d5665bd0ecce849ec422ac 100644
--- a/modules/local/hicstuff/build_matrix_cool_alt.nf
+++ b/modules/local/hicstuff/build_matrix_cool_alt.nf
@@ -3,7 +3,7 @@ process BUILD_MATRIX_COOL_ALT {
label 'process_single'
conda "conda-forge::python=3.9 conda-forge::biopython=1.80 conda-forge::numpy=1.22.3 conda-forge::matplotlib=3.6.3 conda-forge::pandas=1.5.3"
- container = "lbmc/hicstuff:3.1.3"
+ container = "docker.io/lbmc/hicstuff:3.1.3"
input:
tuple val(meta), path(chromosome_size)
diff --git a/modules/local/hicstuff/distance_law.nf b/modules/local/hicstuff/distance_law.nf
index c87112ce6d3f016e319be21660186b451a184110..9a6ad8e85297314df593eec10f888e3ff1f89e2c 100644
--- a/modules/local/hicstuff/distance_law.nf
+++ b/modules/local/hicstuff/distance_law.nf
@@ -3,7 +3,7 @@ process DISTANCE_LAW {
label 'process_high'
conda "conda-forge::python=3.9 conda-forge::biopython=1.80 conda-forge::numpy=1.22.3 conda-forge::matplotlib=3.6.3 conda-forge::pandas=1.5.3"
- container = "lbmc/hicstuff:3.1.3"
+ container = "docker.io/lbmc/hicstuff:3.1.3"
input:
tuple val(meta1), path(idx_pairs)
diff --git a/modules/local/hicstuff/filter_event.nf b/modules/local/hicstuff/filter_event.nf
index 2fa70512ed1a815d50d61a4b8e3ba35d6eb748b6..777ad50f6804001a77054fcc748670d95e2830af 100644
--- a/modules/local/hicstuff/filter_event.nf
+++ b/modules/local/hicstuff/filter_event.nf
@@ -3,7 +3,7 @@ process FILTER_EVENT {
label 'process_high'
conda "conda-forge::python=3.9 conda-forge::biopython=1.80 conda-forge::numpy=1.22.3 conda-forge::matplotlib=3.6.3 conda-forge::pandas=1.5.3"
- container = "lbmc/hicstuff:3.1.3"
+ container = "docker.io/lbmc/hicstuff:3.1.3"
input:
tuple val(meta1), path(idx_pairs)
diff --git a/modules/local/hicstuff/filter_pcr.nf b/modules/local/hicstuff/filter_pcr.nf
index 57ab0f4312846356f2a5f7ce971ffa8c7511d3c9..0b6800ffa0f28f3b5c9a532f10e1ab23129749d3 100644
--- a/modules/local/hicstuff/filter_pcr.nf
+++ b/modules/local/hicstuff/filter_pcr.nf
@@ -3,7 +3,7 @@ process FILTER_PCR {
label 'process_high'
conda "conda-forge::python=3.9 conda-forge::biopython=1.80 conda-forge::numpy=1.22.3 conda-forge::matplotlib=3.6.3 conda-forge::pandas=1.5.3"
- container = "lbmc/hicstuff:3.1.3"
+ container = "docker.io/lbmc/hicstuff:3.1.3"
input:
tuple val(meta1), path(idx_pairs)
diff --git a/modules/local/hicstuff/fragment_enzyme.nf b/modules/local/hicstuff/fragment_enzyme.nf
index b770ee4b8af0b3914b7e8541ff5002bf260fcd84..855bf48b393070206030380ed732b1af54016727 100644
--- a/modules/local/hicstuff/fragment_enzyme.nf
+++ b/modules/local/hicstuff/fragment_enzyme.nf
@@ -3,7 +3,7 @@ process FRAGMENT_ENZYME {
label "process_single"
conda "conda-forge::python=3.9 conda-forge::biopython=1.80 conda-forge::numpy=1.22.3 conda-forge::matplotlib=3.6.3 conda-forge::pandas=1.5.3"
- container = "lbmc/hicstuff:3.1.3"
+ container = "docker.io/lbmc/hicstuff:3.1.3"
input:
val(digestion)
diff --git a/modules/nf-core/custom/picard/markduplicates/main.nf b/modules/nf-core/custom/picard/markduplicates/main.nf
index eef8c81601a2414f3b1b8a3d5cc7b5303f3e0b76..d7b3567308c8bf1286312fb2f2681d546754321f 100644
--- a/modules/nf-core/custom/picard/markduplicates/main.nf
+++ b/modules/nf-core/custom/picard/markduplicates/main.nf
@@ -5,7 +5,7 @@ process PICARD_MARKDUPLICATES {
conda "bioconda::picard=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
- 'quay.io/biocontainers/picard:3.0.0--hdfd78af_1' }"
+ 'biocontainers/picard:3.0.0--hdfd78af_1' }"
input:
tuple val(meta), path(bam)
diff --git a/modules/nf-core/custom/samtools/index/main.nf b/modules/nf-core/custom/samtools/index/main.nf
deleted file mode 100644
index 05fa9758e6b2f9ce5ab3e7fa2404e9b234947169..0000000000000000000000000000000000000000
--- a/modules/nf-core/custom/samtools/index/main.nf
+++ /dev/null
@@ -1,46 +0,0 @@
-process SAMTOOLS_INDEX {
- tag "$meta.id"
- label 'process_low'
-
- conda "bioconda::samtools=1.17"
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
- 'quay.io/biocontainers/samtools:1.17--h00cdaf9_0' }"
-
- input:
- tuple val(meta), path(input)
-
- output:
- tuple val(meta), path("*.bai") , optional:true, emit: bai
- tuple val(meta), path("*.csi") , optional:true, emit: csi
- tuple val(meta), path("*.crai"), optional:true, emit: crai
- path "versions.yml" , emit: versions
-
- when:
- task.ext.when == null || task.ext.when
-
- script:
- def args = task.ext.args ?: ''
- """
- samtools \\
- index \\
- -@ ${task.cpus-1} \\
- $args \\
- $input
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
- END_VERSIONS
- """
-
- stub:
- """
- touch ${input}.bai
- touch ${input}.crai
- touch ${input}.csi
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
- END_VERSIONS
- """
-}
\ No newline at end of file
diff --git a/modules/nf-core/custom/samtools/index/meta.yml b/modules/nf-core/custom/samtools/index/meta.yml
deleted file mode 100644
index 6037b9e658387998214f987017d0bc742156b553..0000000000000000000000000000000000000000
--- a/modules/nf-core/custom/samtools/index/meta.yml
+++ /dev/null
@@ -1,53 +0,0 @@
-name: samtools_index
-description: Index SAM/BAM/CRAM file
-keywords:
- - index
- - bam
- - sam
- - cram
-tools:
- - samtools:
- description: |
- SAMtools is a set of utilities for interacting with and post-processing
- short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
- These files are generated as output by short read aligners like BWA.
- homepage: http://www.htslib.org/
- documentation: http://www.htslib.org/doc/samtools.html
- doi: 10.1093/bioinformatics/btp352
- licence: ["MIT"]
-input:
- - meta:
- type: map
- description: |
- Groovy Map containing sample information
- e.g. [ id:'test', single_end:false ]
- - bam:
- type: file
- description: BAM/CRAM/SAM file
- pattern: "*.{bam,cram,sam}"
-output:
- - meta:
- type: map
- description: |
- Groovy Map containing sample information
- e.g. [ id:'test', single_end:false ]
- - bai:
- type: file
- description: BAM/CRAM/SAM index file
- pattern: "*.{bai,crai,sai}"
- - crai:
- type: file
- description: BAM/CRAM/SAM index file
- pattern: "*.{bai,crai,sai}"
- - csi:
- type: file
- description: CSI index file
- pattern: "*.{csi}"
- - versions:
- type: file
- description: File containing software versions
- pattern: "versions.yml"
-authors:
- - "@drpatelh"
- - "@ewels"
- - "@maxulysse"
\ No newline at end of file
diff --git a/modules/nf-core/custom/samtools/sort/main.nf b/modules/nf-core/custom/samtools/sort/main.nf
index f5692575cb24910127b33e243b7cb29f7535c1c7..b2bbfe1dc6e07f1303def163a1cc3655d434f088 100644
--- a/modules/nf-core/custom/samtools/sort/main.nf
+++ b/modules/nf-core/custom/samtools/sort/main.nf
@@ -5,7 +5,7 @@ process SAMTOOLS_SORT {
conda "bioconda::samtools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
- 'quay.io/biocontainers/samtools:1.17--h00cdaf9_0' }"
+ 'biocontainers/samtools:1.17--h00cdaf9_0' }"
input:
tuple val(meta), path(bam)
diff --git a/modules/nf-core/custom/samtools_n/sort/main.nf b/modules/nf-core/custom/samtools_n/sort/main.nf
index 59a6e2a4e0827332cf3742d2d6e696d299fd4282..740441e1b5cfbfdde4c840650a574e94cb2a8353 100644
--- a/modules/nf-core/custom/samtools_n/sort/main.nf
+++ b/modules/nf-core/custom/samtools_n/sort/main.nf
@@ -5,7 +5,7 @@ process SAMTOOLS_SORT_N {
conda "bioconda::samtools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
- 'quay.io/biocontainers/samtools:1.17--h00cdaf9_0' }"
+ 'biocontainers/samtools:1.17--h00cdaf9_0' }"
input:
tuple val(meta), path(bam)
diff --git a/subworkflows/local/filter_pcr_dup.nf b/subworkflows/local/filter_pcr_dup.nf
index 7fb3fa55f498e66c9ebc6cbc386946ce6e3000e9..3530d6fdbae5cd69fe8b1a23d4433bf076abe379 100644
--- a/subworkflows/local/filter_pcr_dup.nf
+++ b/subworkflows/local/filter_pcr_dup.nf
@@ -6,7 +6,6 @@
include { SAMTOOLS_SORT } from '../../modules/nf-core/custom/samtools/sort/main'
include { SAMTOOLS_SORT_N } from '../../modules/nf-core/custom/samtools_n/sort/main'
include { FILTER_PAIR } from '../../modules/local/filterbam/main'
-include { SAMTOOLS_INDEX } from '../../modules/nf-core/custom/samtools/index/main'
include { PICARD_MARKDUPLICATES } from '../../modules/nf-core/custom/picard/markduplicates/main'
workflow FILTER_PCR_DUP {