Skip to content

Commit

Permalink
add resources and update script
Browse files Browse the repository at this point in the history
  • Loading branch information
@rmcolq
rmcolq committed Nov 23, 2023
1 parent be76406 commit 5e4525b
Show file tree
Hide file tree
Showing 10 changed files with 1,517 additions and 22 deletions.
3 changes: 3 additions & 0 deletions .gitignore
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
work/*
.idea
.nextflow*
15 changes: 7 additions & 8 deletions main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,12 +7,9 @@ process ampliClean {


output:
path "${key}.RSVA.fastq.gz"
val base
tuple val(key), path("${key}.RSVA.fastq.gz")

script:
base = key
println key
"""
ampli_clean -f ${samples} -r ${refs} -o ${key} -b ${bed} -s --fastq
"""
Expand All @@ -21,26 +18,28 @@ process ampliClean {
process articMinion {
container "${params.wf.container}@${params.wf.container_sha}"
input:
path input_reads
val base
tuple val(base), path(input_reads)
path schemes_dir

output:
path "${base}.consensus.fasta"

"""
artic minion --medaka --threads 12 --scheme-directory /home/dmmalone/primer-schemes/ --read-file ${input_reads} --medaka-model r941_min_high_g303 RSVA/V1 ${base}
artic minion --medaka --threads 12 --scheme-directory ${schemes_dir} --read-file ${input_reads} --medaka-model r941_min_high_g303 RSVA/V1 ${base}
"""
}

workflow {
ref_ch = file(params.refs)
bed_ch = file(params.bed)
schemes_dir_ch = file(params.schemes_dir)
fastqIn_ch = Channel.fromPath(params.fastq, checkIfExists:true)
| map { file ->
def key = file.parent.toString().tokenize('/').last()
return tuple(key, file)
} \
| groupTuple()

ampliClean(fastqIn_ch, ref_ch, bed_ch) | articMinion
ampliClean(fastqIn_ch, ref_ch, bed_ch)
articMinion(ampliClean.out, schemes_dir_ch)
}
34 changes: 23 additions & 11 deletions nextflow.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +9,27 @@
//
// for further help editing this file.

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')

params {
help = false
version = false
// Boilerplate options
outdir = "output"
tracedir = "${params.outdir}/pipeline_info/${trace_timestamp}"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
validate_params = true
show_hidden_params = false
schema_ignore_params = false

refs = "resources/RSV_refs.fasta"
bed = "resources/RSVA"
bed = "resources/RSVA/V1/RSVA.primer.bed"
schemes_dir = "resources/"
fastq = null

wf {
Expand All @@ -23,7 +38,7 @@ params {
]
agent = null
container = "rmcolq/artic_rsv"
container_sha = "sha256:68100b5e1d4dc995d707ee716bda9373e827879904c381b59a71105476c36f58"
container_sha = "sha256:ce049e449ed09e8538d246fb2e7a8fb3a58d883092293c7f689ab445e5596cb2"
}
}

Expand All @@ -42,9 +57,6 @@ profiles {
standard {
docker {
enabled = true
// this ensures container is run as host user and group, but
// also adds host user to the within-container group
runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
}
}
debug {
Expand Down Expand Up @@ -158,19 +170,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']

timeline {
enabled = true
file = "${params.tracedir}/execution_timeline_${params.unique_id}.html"
file = "${params.tracedir}/execution_timeline.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report_${params.unique_id}.html"
file = "${params.tracedir}/execution_report.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace_${params.unique_id}.txt"
file = "${params.tracedir}/execution_trace.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag_${params.unique_id}.html"
file = "${params.tracedir}/pipeline_dag.html"
}


Expand Down
9 changes: 6 additions & 3 deletions nextflow_schema.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,14 +30,17 @@
"type": "string",
"title": "Primer bed file",
"description": ""
},
"schemes_dir": {
"type": "string",
"title": "Directory for primer schemes",
"description": ""
}
},
"allOf": [
{
"required": [
"fastq",
"bed",
"ref"
"fastq"
]
}
]
Expand Down
100 changes: 100 additions & 0 deletions resources/RSVA/V1/RSVA.primer.bed
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,100 @@
RSVA 44 66 RSVA_1_LEFT 1 +
RSVA 434 464 RSVA_1_RIGHT 1 -
RSVA 359 385 RSVA_2_LEFT 2 +
RSVA 749 773 RSVA_2_RIGHT 2 -
RSVA 669 699 RSVA_3_LEFT 1 +
RSVA 1057 1083 RSVA_3_RIGHT 1 -
RSVA 990 1016 RSVA_4_LEFT 2 +
RSVA 1366 1389 RSVA_4_RIGHT 2 -
RSVA 1302 1330 RSVA_5_LEFT 1 +
RSVA 1678 1706 RSVA_5_RIGHT 1 -
RSVA 1607 1629 RSVA_6_LEFT 2 +
RSVA 1996 2022 RSVA_6_RIGHT 2 -
RSVA 1935 1957 RSVA_7_LEFT 1 +
RSVA 2313 2336 RSVA_7_RIGHT 1 -
RSVA 2203 2225 RSVA_8_LEFT 2 +
RSVA 2575 2599 RSVA_8_RIGHT 2 -
RSVA 2508 2532 RSVA_9_LEFT 1 +
RSVA 2881 2904 RSVA_9_RIGHT 1 -
RSVA 2729 2755 RSVA_10_LEFT 2 +
RSVA 3115 3137 RSVA_10_RIGHT 2 -
RSVA 3052 3077 RSVA_11_LEFT 1 +
RSVA 3434 3456 RSVA_11_RIGHT 1 -
RSVA 3365 3393 RSVA_12_LEFT 2 +
RSVA 3750 3775 RSVA_12_RIGHT 2 -
RSVA 3689 3714 RSVA_13_LEFT 1 +
RSVA 4065 4092 RSVA_13_RIGHT 1 -
RSVA 3993 4023 RSVA_14_LEFT 2 +
RSVA 4374 4402 RSVA_14_RIGHT 2 -
RSVA 4290 4317 RSVA_15_LEFT 1 +
RSVA 4681 4704 RSVA_15_RIGHT 1 -
RSVA 4622 4644 RSVA_16_LEFT 2 +
RSVA 5002 5024 RSVA_16_RIGHT 2 -
RSVA 4935 4957 RSVA_17_LEFT 1 +
RSVA 5323 5345 RSVA_17_RIGHT 1 -
RSVA 5171 5192 RSVA_18_LEFT 2 +
RSVA 5552 5575 RSVA_18_RIGHT 2 -
RSVA 5450 5472 RSVA_19_LEFT 1 +
RSVA 5825 5855 RSVA_19_RIGHT 1 -
RSVA 5750 5776 RSVA_20_LEFT 2 +
RSVA 6134 6155 RSVA_20_RIGHT 2 -
RSVA 6032 6057 RSVA_21_LEFT 1 +
RSVA 6407 6435 RSVA_21_RIGHT 1 -
RSVA 6345 6370 RSVA_22_LEFT 2 +
RSVA 6729 6752 RSVA_22_RIGHT 2 -
RSVA 6648 6671 RSVA_23_LEFT 1 +
RSVA 7015 7037 RSVA_23_RIGHT 1 -
RSVA 6947 6971 RSVA_24_LEFT 2 +
RSVA 7323 7345 RSVA_24_RIGHT 2 -
RSVA 7241 7269 RSVA_25_LEFT 1 +
RSVA 7625 7647 RSVA_25_RIGHT 1 -
RSVA 7518 7547 RSVA_26_LEFT 2 +
RSVA 7915 7937 RSVA_26_RIGHT 2 -
RSVA 7833 7855 RSVA_27_LEFT 1 +
RSVA 8203 8234 RSVA_27_RIGHT 1 -
RSVA 8131 8157 RSVA_28_LEFT 2 +
RSVA 8521 8546 RSVA_28_RIGHT 2 -
RSVA 8440 8472 RSVA_29_LEFT 1 +
RSVA 8816 8849 RSVA_29_RIGHT 1 -
RSVA 8719 8749 RSVA_30_LEFT 2 +
RSVA 9105 9127 RSVA_30_RIGHT 2 -
RSVA 9032 9058 RSVA_31_LEFT 1 +
RSVA 9412 9439 RSVA_31_RIGHT 1 -
RSVA 9321 9350 RSVA_32_LEFT 2 +
RSVA 9697 9726 RSVA_32_RIGHT 2 -
RSVA 9632 9658 RSVA_33_LEFT 1 +
RSVA 10009 10036 RSVA_33_RIGHT 1 -
RSVA 9948 9973 RSVA_34_LEFT 2 +
RSVA 10327 10354 RSVA_34_RIGHT 2 -
RSVA 10236 10269 RSVA_35_LEFT 1 +
RSVA 10617 10642 RSVA_35_RIGHT 1 -
RSVA 10537 10565 RSVA_36_LEFT 2 +
RSVA 10920 10950 RSVA_36_RIGHT 2 -
RSVA 10849 10872 RSVA_37_LEFT 1 +
RSVA 11227 11257 RSVA_37_RIGHT 1 -
RSVA 11154 11181 RSVA_38_LEFT 2 +
RSVA 11535 11559 RSVA_38_RIGHT 2 -
RSVA 11454 11477 RSVA_39_LEFT 1 +
RSVA 11819 11852 RSVA_39_RIGHT 1 -
RSVA 11746 11768 RSVA_40_LEFT 2 +
RSVA 12130 12158 RSVA_40_RIGHT 2 -
RSVA 12055 12085 RSVA_41_LEFT 1 +
RSVA 12448 12472 RSVA_41_RIGHT 1 -
RSVA 12385 12411 RSVA_42_LEFT 2 +
RSVA 12766 12792 RSVA_42_RIGHT 2 -
RSVA 12683 12707 RSVA_43_LEFT 1 +
RSVA 13067 13093 RSVA_43_RIGHT 1 -
RSVA 12995 13022 RSVA_44_LEFT 2 +
RSVA 13376 13398 RSVA_44_RIGHT 2 -
RSVA 13309 13334 RSVA_45_LEFT 1 +
RSVA 13694 13721 RSVA_45_RIGHT 1 -
RSVA 13589 13616 RSVA_46_LEFT 2 +
RSVA 13972 14005 RSVA_46_RIGHT 2 -
RSVA 13902 13929 RSVA_47_LEFT 1 +
RSVA 14289 14317 RSVA_47_RIGHT 1 -
RSVA 14222 14247 RSVA_48_LEFT 2 +
RSVA 14606 14632 RSVA_48_RIGHT 2 -
RSVA 14549 14570 RSVA_49_LEFT 1 +
RSVA 14925 14951 RSVA_49_RIGHT 1 -
RSVA 14739 14768 RSVA_50_LEFT 2 +
RSVA 15114 15147 RSVA_50_RIGHT 2 -
Loading

0 comments on commit 5e4525b

Please sign in to comment.