fixup! * When running differential expression or feature counting, RN…

…Alysis session reports will automatically include a logfile with R session info. * Added optional parameters to all differential expression functions, allowing users to return a path to a logfile with R session info.

tests/test_files/fastq_pipeline_tests/paired/truth/01_trim_adapters_paired_end/cutadapt_log_reads_1_reads_2.log

@@ -0,0 +1,144 @@
+This is cutadapt 4.9 with Python 3.12.3
+
+Command line parameters: -a ATGGGTATATGGGT -A AGTTTACCGTTGT --quality-cutoff 20 --minimum-length 10 --trim-n --cores 0 --overlap 3 --error-rate 0.1 --pair-filter=any --output tests/test_files/fastq_pipeline_tests/paired/outdir/01_trim_adapters_paired_end/reads_1_trimmed.fastq --paired-output tests/test_files/fastq_pipeline_tests/paired/outdir/01_trim_adapters_paired_end/reads_2_trimmed.fastq tests/test_files/fastq_pipeline_tests/in/reads_1.fastq tests/test_files/fastq_pipeline_tests/in/reads_2.fastq
+
+Processing paired-end reads on 12 cores ...
+
+Finished in 2.095 s (209.489 �s/read; 0.29 M reads/minute).
+
+
+
+=== Summary ===
+
+
+
+Total read pairs processed:             10,000
+
+  Read 1 with adapter:                     163 (1.6%)
+
+  Read 2 with adapter:                     185 (1.8%)
+
+
+
+== Read fate breakdown ==
+
+Pairs that were too short:                   3 (0.0%)
+
+Pairs written (passing filters):         9,997 (100.0%)
+
+
+
+Total basepairs processed:     1,000,112 bp
+
+  Read 1:       500,042 bp
+
+  Read 2:       500,070 bp
+
+Quality-trimmed:                       0 bp (0.0%)
+
+  Read 1:             0 bp
+
+  Read 2:             0 bp
+
+Total written (filtered):        998,560 bp (99.8%)
+
+  Read 1:       499,313 bp
+
+  Read 2:       499,247 bp
+
+
+
+=== First read: Adapter 1 ===
+
+
+
+Sequence: ATGGGTATATGGGT; Type: regular 3'; Length: 14; Trimmed: 163 times
+
+
+
+Minimum overlap: 3
+
+No. of allowed errors:
+
+1-9 bp: 0; 10-14 bp: 1
+
+
+
+Bases preceding removed adapters:
+
+  A: 28.8%
+
+  C: 37.4%
+
+  G: 17.8%
+
+  T: 14.1%
+
+  none/other: 1.8%
+
+
+
+Overview of removed sequences
+
+length	count	expect	max.err	error counts
+
+3	116	156.2	0	116
+
+4	32	39.1	0	32
+
+5	11	9.8	0	11
+
+6	1	2.4	0	1
+
+64	3	0.0	1	3
+
+
+
+
+
+=== Second read: Adapter 2 ===
+
+
+
+Sequence: AGTTTACCGTTGT; Type: regular 3'; Length: 13; Trimmed: 185 times
+
+
+
+Minimum overlap: 3
+
+No. of allowed errors:
+
+1-9 bp: 0; 10-13 bp: 1
+
+
+
+Bases preceding removed adapters:
+
+  A: 27.0%
+
+  C: 28.1%
+
+  G: 31.4%
+
+  T: 13.5%
+
+  none/other: 0.0%
+
+
+
+Overview of removed sequences
+
+length	count	expect	max.err	error counts
+
+3	124	156.2	0	124
+
+4	40	39.1	0	40
+
+5	18	9.8	0	18
+
+6	1	2.4	0	1
+
+7	1	0.6	0	1
+
+10	1	0.0	1	0 1
+

tests/test_files/fastq_pipeline_tests/paired/truth/03_featurecounts_paired_end/logfile.log

@@ -0,0 +1,71 @@
+
+        ==========     _____ _    _ ____  _____  ______          _____
+        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \
+          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
+            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
+              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
+        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
+       Rsubread 2.14.2
+
+//========================== featureCounts setting ===========================\\
+||                                                                            ||
+||             Input files : 1 SAM file                                       ||
+||                                                                            ||
+||                           reads_.sam                                       ||
+||                                                                            ||
+||              Paired-end : yes                                              ||
+||        Count read pairs : yes                                              ||
+||              Annotation : transcripts.gtf (GTF)                            ||
+||      Dir for temp files : .                                                ||
+||                 Threads : 1                                                ||
+||                   Level : meta-feature level                               ||
+||      Multimapping reads : not counted                                      ||
+||     Multiple alignments : primary alignment only                           ||
+|| Multi-overlapping reads : not counted                                      ||
+||   Min overlapping bases : 1                                                ||
+||                                                                            ||
+\\============================================================================//
+
+//================================= Running ==================================\\
+||                                                                            ||
+|| Load annotation file transcripts.gtf ...                                   ||
+||    Features : 79                                                           ||
+||    Meta-features : 11                                                      ||
+||    Chromosomes/contigs : 2                                                 ||
+||                                                                            ||
+|| Process SAM file reads_.sam...                                             ||
+||    Paired-end reads are included.                                          ||
+||    Total alignments : 9997                                                 ||
+||    Successfully assigned alignments : 0 (0.0%)                             ||
+||    Running time : 0.00 minutes                                             ||
+||                                                                            ||
+|| Write the final count table.                                               ||
+|| Write the read assignment summary.                                         ||
+||                                                                            ||
+\\============================================================================//
+
+R version 4.3.1 (2023-06-16 ucrt)
+Platform: x86_64-w64-mingw32/x64 (64-bit)
+Running under: Windows 11 x64 (build 22631)
+
+Matrix products: default
+
+
+locale:
+[1] LC_COLLATE=English_United States.utf8
+[2] LC_CTYPE=English_United States.utf8
+[3] LC_MONETARY=English_United States.utf8
+[4] LC_NUMERIC=C
+[5] LC_TIME=English_United States.utf8
+
+time zone: Asia/Jerusalem
+tzcode source: internal
+
+attached base packages:
+[1] stats     graphics  grDevices utils     datasets  methods   base
+
+other attached packages:
+[1] Rsubread_2.14.2
+
+loaded via a namespace (and not attached):
+[1] compiler_4.3.1 Matrix_1.6-1.1 grid_4.3.1     lattice_0.21-9

tests/test_files/fastq_pipeline_tests/single/truth/01_trim_adapters_single_end/cutadapt_log_reads_1.log

@@ -0,0 +1,80 @@
+This is cutadapt 4.9 with Python 3.12.3
+
+Command line parameters: --adapter ATGGGTATATGGGT --quality-cutoff 20 --minimum-length 10 --trim-n --cores 0 --overlap 3 --error-rate 0.1 --output tests/test_files/fastq_pipeline_tests/single/outdir/01_trim_adapters_single_end/reads_1_trimmed.fastq tests/test_files/fastq_pipeline_tests/in/reads_1.fastq
+
+Processing single-end reads on 12 cores ...
+
+Finished in 2.048 s (204.823 �s/read; 0.29 M reads/minute).
+
+
+
+=== Summary ===
+
+
+
+Total reads processed:                  10,000
+
+Reads with adapters:                       163 (1.6%)
+
+
+
+== Read fate breakdown ==
+
+Reads that were too short:                   3 (0.0%)
+
+Reads written (passing filters):         9,997 (100.0%)
+
+
+
+Total basepairs processed:       500,042 bp
+
+Quality-trimmed:                       0 bp (0.0%)
+
+Total written (filtered):        499,313 bp (99.9%)
+
+
+
+=== Adapter 1 ===
+
+
+
+Sequence: ATGGGTATATGGGT; Type: regular 3'; Length: 14; Trimmed: 163 times
+
+
+
+Minimum overlap: 3
+
+No. of allowed errors:
+
+1-9 bp: 0; 10-14 bp: 1
+
+
+
+Bases preceding removed adapters:
+
+  A: 28.8%
+
+  C: 37.4%
+
+  G: 17.8%
+
+  T: 14.1%
+
+  none/other: 1.8%
+
+
+
+Overview of removed sequences
+
+length	count	expect	max.err	error counts
+
+3	116	156.2	0	116
+
+4	32	39.1	0	32
+
+5	11	9.8	0	11
+
+6	1	2.4	0	1
+
+64	3	0.0	1	3
+

tests/test_files/fastq_pipeline_tests/single/truth/01_trim_adapters_single_end/cutadapt_log_reads_2.log

@@ -0,0 +1,80 @@
+This is cutadapt 4.9 with Python 3.12.3
+
+Command line parameters: --adapter ATGGGTATATGGGT --quality-cutoff 20 --minimum-length 10 --trim-n --cores 0 --overlap 3 --error-rate 0.1 --output tests/test_files/fastq_pipeline_tests/single/outdir/01_trim_adapters_single_end/reads_2_trimmed.fastq tests/test_files/fastq_pipeline_tests/in/reads_2.fastq
+
+Processing single-end reads on 12 cores ...
+
+Finished in 2.189 s (218.890 �s/read; 0.27 M reads/minute).
+
+
+
+=== Summary ===
+
+
+
+Total reads processed:                  10,000
+
+Reads with adapters:                       164 (1.6%)
+
+
+
+== Read fate breakdown ==
+
+Reads that were too short:                   5 (0.1%)
+
+Reads written (passing filters):         9,995 (100.0%)
+
+
+
+Total basepairs processed:       500,070 bp
+
+Quality-trimmed:                       0 bp (0.0%)
+
+Total written (filtered):        499,234 bp (99.8%)
+
+
+
+=== Adapter 1 ===
+
+
+
+Sequence: ATGGGTATATGGGT; Type: regular 3'; Length: 14; Trimmed: 164 times
+
+
+
+Minimum overlap: 3
+
+No. of allowed errors:
+
+1-9 bp: 0; 10-14 bp: 1
+
+
+
+Bases preceding removed adapters:
+
+  A: 27.4%
+
+  C: 29.9%
+
+  G: 21.3%
+
+  T: 18.3%
+
+  none/other: 3.0%
+
+
+
+Overview of removed sequences
+
+length	count	expect	max.err	error counts
+
+3	127	156.2	0	127
+
+4	26	39.1	0	26
+
+5	5	9.8	0	5
+
+6	1	2.4	0	1
+
+64	5	0.0	1	5
+