change default parameter values of FASTP max

length and three prime adapter sequence, set adapter fasta based on with_umi parameter, change included adapter fasta
nf-core · Feb 2, 2024 · f83f0a5 · f83f0a5
1 parent 8c1143d
commit f83f0a5
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Showing 4 changed files with 16 additions and 10 deletions.
diff --git a/assets/known_adapters.fa b/assets/known_adapters.fa
@@ -1,2 +1,6 @@
-> Illumina Sequencing Adapter
+> QIAseq miRNA adapter
+AACTGTAGGCACCATCAAT
+> Illumina miRNA adapter
+TGGAATTCTCGGGTGCCAAGG
+> Nextflex miRNA adapter
 TGGAATTCTCGGGTGCCAAGG
diff --git a/conf/modules.config b/conf/modules.config
@@ -47,11 +47,11 @@ process {
     //
     withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' {
         ext.args = [ "",
-            params.trim_fastq              ? "" : "--disable_adapter_trimming",
-            params.clip_r1 > 0             ? "--trim_front1 ${params.clip_r1}" : "", // Remove bp from the 5' end of read 1.
-            params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
-            params.fastp_min_length > 0    ? "-l ${params.fastp_min_length}" : "",
-            params.fastp_max_length > 0    ? "--max_len1 ${params.fastp_max_length}" : "",
+            params.trim_fastq                  ? "" : "--disable_adapter_trimming",
+            params.clip_r1 > 0                 ? "--trim_front1 ${params.clip_r1}" : "", // Remove bp from the 5' end of read 1.
+            params.three_prime_clip_r1 > 0     ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
+            params.fastp_min_length > 0        ? "-l ${params.fastp_min_length}" : "",
+            params.fastp_max_length > 0        ? "--max_len1 ${params.fastp_max_length}" : "",
             params.three_prime_adapter == null ?  '' : "--adapter_sequence ${params.three_prime_adapter}"
         ].join(" ").trim()
         publishDir = [

diff --git a/nextflow.config b/nextflow.config
@@ -41,7 +41,7 @@ params {
     // Trimming options
     clip_r1                     = null
     three_prime_clip_r1         = null
-    three_prime_adapter         = null
+    three_prime_adapter         = 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCA'
     trim_fastq                  = true
     fastp_min_length            = 17
     fastp_known_mirna_adapters  = "$projectDir/assets/known_adapters.fa"
@@ -52,7 +52,7 @@ params {
     skip_mirdeep                = false
     skip_fastp                  = false
     save_reference              = false
-    fastp_max_length            = 40
+    fastp_max_length            = 100
     min_trimmed_reads           = 10
 
     // Contamination filtering

diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
@@ -134,6 +134,8 @@ workflow SMRNASEQ {
     .set { ch_cat_fastq }
     ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null))
 
+    mirna_adapters = params.with_umi ? [] : params.fastp_known_mirna_adapters
+
     //
     // SUBWORKFLOW: Read QC, extract UMI and trim adapters & dedup UMIs if necessary / desired by the user
     //
@@ -144,7 +146,7 @@ workflow SMRNASEQ {
         params.skip_umi_extract,
         params.umi_discard_read,
         params.skip_fastp,
-        params.fastp_known_mirna_adapters,
+        mirna_adapters,
         params.save_trimmed_fail,
         params.save_merged,
         params.min_trimmed_reads
@@ -184,7 +186,7 @@ workflow SMRNASEQ {
         // Filter out sequences smaller than params.fastp_min_length
         FASTP_LENGTH_FILTER (
             UMITOOLS_EXTRACT.out.reads,
-            params.fastp_known_mirna_adapters,
+            mirna_adapters,
             params.save_trimmed_fail,
             params.save_merged
         )