Merge pull request #1294 from atrigila/smrnaseq

Add smrnaseq trimmed fastq test data

samplesheet/v2.0/samplesheet_skipfastp.csv

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+sample,fastq_1
+Clone1_N1,https://github.com/nf-core/test-datasets/raw/smrnaseq/testdata/trimmed/small_Clone1_N1.fastp.fastq.gz
+Clone1_N3,https://github.com/nf-core/test-datasets/raw/smrnaseq/testdata/trimmed/small_Clone1_N3.fastp.fastq.gz

testdata/README.md

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+The data in this directory contains input files to start the pipeline from different protocols or settings.
+1. Trimmed reads obtained from fastp. Useful to test the pipeline with the flag `--skip_fastp`: `trimmed` directory

testdata/trimmed/README.md

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+Sample data from FASTP. This data was obtained running `nextflow run smrnaseq -profile test,docker -r dev --save_merged` with the following custom `publishDir`:
+
+```
+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.three_prime_adapter == "auto-detect" ?  "" : "--adapter_sequence ${params.three_prime_adapter}"
+        ].join(" ").trim()
+        publishDir = [
+            [
+                path: { "${params.outdir}/fastp/fastq" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fastp.fastq.gz",
+                enabled: params.save_merged
+            ]
+        ]
+    }
+```
+
+Size was reduced with: `zcat Clone1_N3.fastp.fastq.gz | head -n 4000000 | gzip > small_Clone1_N3.fastp.fastq.gz`