Skip to content

Commit

Permalink
fix #7 allow to use remote files for reads, genome and annotations
Browse files Browse the repository at this point in the history
  • Loading branch information
@Juke34
Juke34 committed Jan 13, 2025
1 parent 4f5b0a1 commit 2703804
Show file tree
Hide file tree
Showing 4 changed files with 88 additions and 82 deletions.
136 changes: 86 additions & 50 deletions aline.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -120,21 +120,25 @@ if( ! params.library_type.contains("auto") ){
}

// ---- check annotation file
def annotation_file = ""
def annotation_file
if (params.annotation){
File f = new File( "${params.annotation}" );
if (! f.exists() ){
log.error "Warning: Annotation file <${params.annotation}> does not exist.\n"
stop_pipeline = true
if (params.annotation.startsWith('http:') || params.annotation.startsWith('https:') || params.annotation.startsWith('s3:') || params.annotation.startsWith('az:') || params.annotation.startsWith('gs:') || params.annotation.startsWith('ftp:') ) {
annotation_file = file(params.annotation)
annotation_file = annotation_file.getName()
} else {
File f = new File( "${params.annotation}" );
if (! f.exists() ){
log.error "Warning: Annotation file <${params.annotation}> does not exist.\n"
stop_pipeline = true
}
annotation_file = f.getName()
}
annotation_file = f.getName()
}

// ----------------------------------------------------------

log.info """check alinger parameters ..."""


// --- bbmap tool ---
if ("bbmap" in aligner_list && !params.relax){
if (params.read_type == "pacbio" || params.read_type == "ont"){
Expand Down Expand Up @@ -321,6 +325,7 @@ log.info """
General Parameters
genome : ${params.genome}
reads : ${params.reads}
annotation : ${params.annotation}
aligner : ${params.aligner}
read_type : ${params.read_type}
paired_reads_pattern : ${params.paired_reads_pattern}
Expand All @@ -339,7 +344,6 @@ log.info printAlignerOptions(aligner_list, annotation_file, params.star_index_op
//*************************************************
// STEP 2 - Include needed modules
//*************************************************
include {prepare_annotation} from "$baseDir/modules/bash.nf"
include {bbmap_index; bbmap} from "$baseDir/modules/bbmap.nf"
include {bowtie2_index; bowtie2} from "$baseDir/modules/bowtie2.nf"
include {bwa_index; bwaaln; bwamem; bwasw} from "$baseDir/modules/bwa.nf"
Expand Down Expand Up @@ -383,66 +387,101 @@ if (
) { "executer selected" }
else { exit 1, "No executer selected: -profile docker/singularity"}

// check input (file or folder?)
// --------- handle read input (file or folder / local or remote / paired or not) --------
def list_files = []
def pattern_reads
def fromFilePairs_input
def per_pair = false // read the reads per pair
def path_reads = params.reads

// in case of folder provided, add a trailing slash if missing
File input_reads = new File(path_reads)
if(input_reads.exists()){
if ( input_reads.isDirectory()) {
if (! input_reads.name.endsWith("/")) {
path_reads = "${path_reads}" + "/"
// check if paired reads
def per_pair = false // read the reads per pair
if (params.read_type == "short_paired") {
per_pair = true
}

// Case of remote data
def via_URL = false
def read_list=[]
if (path_reads.startsWith('https:') || path_reads.startsWith('s3:') || path_reads.startsWith('az:') || path_reads.startsWith('gs:') || path_reads.startsWith('ftp:') ) {
log.info "The input is a based on URLs! ${path_reads}\n"
via_URL = true
str_list = path_reads.tokenize(',')
str_list.each {
str_list2 = it.tokenize(' ')
str_list2.each {
read_list.add(file(it)) // use file insted of File for URL
}
}
fromFilePairs_input = read_list
}
// Case of local data
else {
File input_reads = file(path_reads)
if(input_reads.exists()){
if ( input_reads.isDirectory()) {
// in case of folder provided, add a trailing slash if missing
if (! input_reads.name.endsWith("/")) {
path_reads = "${path_reads}" + "/"
}
}
}

if (params.read_type == "short_paired") {
per_pair = true
pattern_reads = "${params.paired_reads_pattern}${params.reads_extension}"
fromFilePairs_input = "${path_reads}*${params.paired_reads_pattern}${params.reads_extension}"
} else{
pattern_reads = "${params.reads_extension}"
fromFilePairs_input = "${path_reads}*${params.reads_extension}"
}
if (params.read_type == "short_paired") {
pattern_reads = "${params.paired_reads_pattern}${params.reads_extension}"
fromFilePairs_input = "${path_reads}*${params.paired_reads_pattern}${params.reads_extension}"
} else{
pattern_reads = "${params.reads_extension}"
fromFilePairs_input = "${path_reads}*${params.reads_extension}"
}

if(input_reads.exists()){
if ( input_reads.isDirectory()) {
log.info "The input ${path_reads} is a folder!\n"
input_reads.eachFileRecurse(FILES){
if (it.name =~ ~/${pattern_reads}/){
list_files.add(it)
if(input_reads.exists()){
if ( input_reads.isDirectory()) {
log.info "The input ${path_reads} is a folder!\n"
input_reads.eachFileRecurse(FILES){
if (it.name =~ ~/${pattern_reads}/){
list_files.add(it)
}
}
samples_number = list_files.size()
log.info "${samples_number} files in ${path_reads} with pattern ${pattern_reads}"
}
samples_number = list_files.size()
log.info "${samples_number} files in ${path_reads} with pattern ${pattern_reads}"
}
else {
log.info "The input ${path_reads} is a file!\n"
pattern_reads = "${path_reads}"
else {
log.info "The input ${path_reads} is a file!\n"
pattern_reads = "${path_reads}"
}
} else {
exit 1, "The input ${path_reads} does not exists!\n"
}
} else {
exit 1, "The input ${path_reads} does not exists!\n"
}

//*************************************************
// STEP 4 - Main Workflow
//*************************************************

workflow {

main:
def reads
reads = Channel.fromFilePairs(fromFilePairs_input, size: per_pair ? 2 : 1, checkIfExists: true)
.ifEmpty { exit 1, "Cannot find reads matching ${path_reads}!\n" }

// In case of URL paired data, we cannot use fromFilePairs because matching pattern impossible. We must recreate manually a structure similar
if (via_URL && per_pair){
my_samples = Channel.of(read_list)
reads = my_samples.flatten().map { it -> [it.name.split('_')[0], it] }
.groupTuple()
.ifEmpty { exit 1, "Cannot find reads matching ${path_reads}!\n" }
} else {
reads = Channel.fromFilePairs(fromFilePairs_input, size: per_pair ? 2 : 1, checkIfExists: true)
.ifEmpty { exit 1, "Cannot find reads matching ${path_reads}!\n" }
}

genome = Channel.fromPath(params.genome, checkIfExists: true)
.ifEmpty { exit 1, "Cannot find genome matching ${params.genome}!\n" }

align(reads,genome,aligner_list)

if(annotation_file){
annotation = Channel.fromPath(params.annotation, checkIfExists: true)
.ifEmpty { exit 1, "Cannot find annotation matching ${annotation_file}!\n" }
} else {
annotation = Channel.of("$baseDir/config/aline_null.gtf") // use the fake file (not used by tools just for the processes to be called)
}

align(reads, genome, annotation, aligner_list)
}


Expand All @@ -455,6 +494,7 @@ workflow align {
take:
raw_reads
genome
annotation
aligner_list

main:
Expand All @@ -465,10 +505,6 @@ workflow align {
// PREPROCESSING
// ------------------------------------------------------------------------------------------------

// Prepare annotation
prepare_annotation(params.annotation)
prepare_annotation.out.set{annotation}

// ------------------- QC -----------------
if(params.fastqc){
fastqc_raw(raw_reads, "fastqc/raw", "raw")
Expand Down Expand Up @@ -830,7 +866,7 @@ def helpMSG() {
--novoalign_license license for novoalign. You can ask for one month free trial license at http://www.novocraft.com/products/novoalign/
--nucmer_options additional options for nucmer
--star_options additional options for star
--star_2pass set to true to run STAR in 2pass mode (default: false)
--star_2pass set to true to run STAR in 2pass mode (default: false)
--read_length [Optional][used by STAR] length of the reads, if none provided it is automatically deduced
--subread_options additional options for subread
--sublong_options additional options for sublong
Expand Down
1 change: 1 addition & 0 deletions config/aline_null.gtf
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
# This file is necessary, it is used as a dummy file. It is not intended to be used by tools but just to allow processes to be called when no real annotation file is provided.
31 changes: 0 additions & 31 deletions modules/bash.nf
View file

This file was deleted.

2 changes: 1 addition & 1 deletion modules/star.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ process prepare_star_index_options {
script:
star_index_options = "${params.star_index_options}"

if ( annotation.toString() != "null.gtf" ){
if ( annotation.toString() != "aline_null.gtf" ){
// Deal with --sjdbGTFfile option
if( !star_index_options.contains("--sjdbGTFfile") ){
star_index_options += " --sjdbGTFfile ${annotation}"
Expand Down

0 comments on commit 2703804

Please sign in to comment.