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Update nextflow.config
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drpatelh
parent
f32950d0f2
commit
4df72f0396
5 changed files with 25 additions and 201 deletions
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@ -1,2 +1,25 @@
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// docker.enabled = true
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params.outdir = './results'
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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clip_r1 = 0
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clip_r2 = 0
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three_prime_clip_r1 = 0
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three_prime_clip_r2 = 0
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}
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profiles {
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conda {
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params.conda = true
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}
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docker {
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docker.enabled = true
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docker.runOptions = '-u \$(id -u):\$(id -g)'
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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}
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}
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@ -1,97 +0,0 @@
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SUMMARISING RUN PARAMETERS
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==========================
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Input filename: test_R1.fastq.gz
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Trimming mode: paired-end
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Trim Galore version: 0.6.5
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Cutadapt version: 2.3
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Number of cores used for trimming: 1
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Quality Phred score cutoff: 20
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Quality encoding type selected: ASCII+33
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Using Nextera adapter for trimming (count: 83). Second best hit was smallRNA (count: 0)
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Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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Maximum trimming error rate: 0.1 (default)
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Minimum required adapter overlap (stringency): 1 bp
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Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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Output file will be GZIP compressed
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This is cutadapt 2.3 with Python 3.7.3
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Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA test_R1.fastq.gz
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Processing reads on 1 core in single-end mode ...
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Finished in 0.19 s (19 us/read; 3.12 M reads/minute).
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=== Summary ===
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Total reads processed: 10,000
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Reads with adapters: 3,225 (32.2%)
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Reads written (passing filters): 10,000 (100.0%)
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Total basepairs processed: 760,000 bp
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Quality-trimmed: 4,492 bp (0.6%)
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Total written (filtered): 748,403 bp (98.5%)
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=== Adapter 1 ===
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Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 3225 times.
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No. of allowed errors:
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0-9 bp: 0; 10-12 bp: 1
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Bases preceding removed adapters:
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A: 23.8%
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C: 28.2%
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G: 22.7%
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T: 25.3%
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none/other: 0.0%
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Overview of removed sequences
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length count expect max.err error counts
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1 2170 2500.0 0 2170
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2 622 625.0 0 622
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3 223 156.2 0 223
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4 64 39.1 0 64
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5 14 9.8 0 14
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6 9 2.4 0 9
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7 8 0.6 0 8
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8 5 0.2 0 5
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9 4 0.0 0 4
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10 8 0.0 1 7 1
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11 3 0.0 1 3
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12 4 0.0 1 4
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13 6 0.0 1 6
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14 5 0.0 1 4 1
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15 5 0.0 1 5
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16 6 0.0 1 5 1
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17 3 0.0 1 3
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18 3 0.0 1 3
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19 1 0.0 1 1
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20 3 0.0 1 3
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21 7 0.0 1 7
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22 7 0.0 1 7
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23 3 0.0 1 3
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24 6 0.0 1 6
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25 4 0.0 1 4
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26 2 0.0 1 2
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27 4 0.0 1 4
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28 1 0.0 1 1
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29 3 0.0 1 3
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30 4 0.0 1 4
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32 3 0.0 1 3
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33 2 0.0 1 1 1
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34 1 0.0 1 1
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35 1 0.0 1 1
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40 1 0.0 1 1
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42 1 0.0 1 0 1
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45 1 0.0 1 0 1
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49 1 0.0 1 0 1
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52 1 0.0 1 0 1
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56 2 0.0 1 0 2
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59 1 0.0 1 0 1
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67 1 0.0 1 0 1
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70 2 0.0 1 0 2
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RUN STATISTICS FOR INPUT FILE: test_R1.fastq.gz
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=============================================
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10000 sequences processed in total
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@ -1 +0,0 @@
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../../../../tests/data/fastq/rna/test_R1_val_1.fq.gz
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@ -1,100 +0,0 @@
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SUMMARISING RUN PARAMETERS
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==========================
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Input filename: test_R2.fastq.gz
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Trimming mode: paired-end
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Trim Galore version: 0.6.5
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Cutadapt version: 2.3
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Number of cores used for trimming: 1
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Quality Phred score cutoff: 20
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Quality encoding type selected: ASCII+33
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Using Nextera adapter for trimming (count: 83). Second best hit was smallRNA (count: 0)
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Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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Maximum trimming error rate: 0.1 (default)
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Minimum required adapter overlap (stringency): 1 bp
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Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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Output file will be GZIP compressed
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This is cutadapt 2.3 with Python 3.7.3
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Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA test_R2.fastq.gz
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Processing reads on 1 core in single-end mode ...
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Finished in 0.22 s (22 us/read; 2.71 M reads/minute).
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=== Summary ===
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Total reads processed: 10,000
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Reads with adapters: 3,295 (33.0%)
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Reads written (passing filters): 10,000 (100.0%)
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Total basepairs processed: 760,000 bp
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Quality-trimmed: 7,096 bp (0.9%)
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Total written (filtered): 745,649 bp (98.1%)
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=== Adapter 1 ===
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Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 3295 times.
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No. of allowed errors:
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0-9 bp: 0; 10-12 bp: 1
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Bases preceding removed adapters:
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A: 22.6%
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C: 28.2%
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G: 23.6%
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T: 25.6%
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none/other: 0.0%
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Overview of removed sequences
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length count expect max.err error counts
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1 2213 2500.0 0 2213
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2 647 625.0 0 647
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3 239 156.2 0 239
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4 53 39.1 0 53
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5 10 9.8 0 10
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6 7 2.4 0 7
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7 8 0.6 0 8
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8 5 0.2 0 5
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9 5 0.0 0 5
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10 10 0.0 1 8 2
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11 2 0.0 1 2
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12 4 0.0 1 4
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13 7 0.0 1 7
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14 3 0.0 1 3
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15 4 0.0 1 4
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16 5 0.0 1 5
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17 3 0.0 1 3
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18 5 0.0 1 4 1
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19 2 0.0 1 1 1
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20 3 0.0 1 3
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21 7 0.0 1 7
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22 6 0.0 1 6
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23 3 0.0 1 3
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24 7 0.0 1 7
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25 4 0.0 1 4
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26 2 0.0 1 2
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27 4 0.0 1 4
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28 1 0.0 1 1
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29 3 0.0 1 3
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30 4 0.0 1 4
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32 3 0.0 1 3
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33 1 0.0 1 1
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34 1 0.0 1 1
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35 2 0.0 1 1 1
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40 1 0.0 1 0 1
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41 1 0.0 1 1
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46 1 0.0 1 0 1
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48 1 0.0 1 0 1
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49 2 0.0 1 0 2
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56 2 0.0 1 0 2
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59 1 0.0 1 0 1
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70 1 0.0 1 0 1
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73 2 0.0 1 0 2
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RUN STATISTICS FOR INPUT FILE: test_R2.fastq.gz
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=============================================
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10000 sequences processed in total
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Total number of sequences analysed for the sequence pair length validation: 10000
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Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21 (0.21%)
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@ -1 +0,0 @@
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../../../../tests/data/fastq/rna/test_R2_val_2.fq.gz
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