review

README.md

@@ -269,17 +269,20 @@ your run.
 # Sample downloads from SRA
 
 An independent Snakemake workflow `workflow/rules/sra_download.smk` is included
-for the download of SRA samples.
+for the download of sequencing libraries from the Sequence Read Archive and
+conversion into FASTQ.
 
-The workflow expects the following config:
-* `samples`, a sample table (tsv) with column *sample* containing *RR* identifiers,
-see example [here](tests/input_files/sra_samples.tsv).
+The workflow expects the following parameters in the configuration file:
+* `samples`, a sample table (tsv) with column *sample* containing *SRR*
+  identifiers (ERR and DRR are also supported), see
+  [example](tests/input_files/sra_samples.tsv).
 * `outdir`, an output directory
-* `samples_out`, a pointer to a modified sample table with location of fastq files
+* `samples_out`, a pointer to a modified sample table with the locations of
+  the corresponding FASTQ files
 * `cluster_log_dir`, the cluster log directory.
 
-For executing the example one can use the following conda execution
-(with activated *zarp* environment):
+For executing the example with Conda environments, one can use the following
+command (from within the activated `zarp` Conda environment):
 
 ```bash
 snakemake --snakefile="workflow/rules/sra_download.smk" \
@@ -290,10 +293,16 @@ snakemake --snakefile="workflow/rules/sra_download.smk" \
                    log_dir="logs" \
                    cluster_log_dir="logs/cluster_log"
 ```
-or the singularity one by replacing ```local-conda``` with ```local-singularity```
-After successful execution, `results/sra_downloads/sra_samples.out.tsv` should contain:
+
+Alternatively, change the argument to `--profile` from `local-conda` to
+`local-singularity` to execute the workflow steps within Singularity
+containers.
+
+After successful execution, `results/sra_downloads/sra_samples.out.tsv` should
+contain:
+
 ```tsv
-ssample  fq1     fq2
+sample  fq1     fq2
 SRR18552868     results/sra_downloads/compress/SRR18552868/SRR18552868.fastq.gz 
 SRR18549672     results/sra_downloads/compress/SRR18549672/SRR18549672_1.fastq.gz       results/sra_downloads/compress/SRR18549672/SRR18549672_2.fastq.gz
 ERR2248142      results/sra_downloads/compress/ERR2248142/ERR2248142.fastq.gz 

tests/test_htsinfer_workflow/test.local.sh

@@ -42,6 +42,4 @@ snakemake \
     --keep-incomplete
 
 # Check md5 sum of some output files
-#find results/ -type f -name \*\.gz -exec gunzip '{}' \;
-#find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
-md5sum --check "expected_output.md5"
+md5sum --check "expected_output.md5"

tests/test_integration_workflow/test.local.sh

@@ -83,4 +83,3 @@ diff \
 diff \
     <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
     <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
-

tests/test_integration_workflow/test.slurm.sh

@@ -82,4 +82,4 @@ diff \
     <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
 diff \
     <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
-    <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+    <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')

tests/test_integration_workflow/test.temp.flag.sh

@@ -41,17 +41,6 @@ find results/ -type f -name \*\.gz -exec gunzip '{}' \;
 find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
 md5sum --check "expected_output_temp_flag.md5"
 
-# Checksum file generated with
-# find results/ \
-#    -type f \
-#    -name \*\.gz \
-#    -exec gunzip '{}' \;
-# find results/ \
-#    -type f \
-#    -name \*\.zip \
-#    -exec sh -c 'unzip -o {} -d $(dirname {})' \;
-# md5sum $(cat expected_output.files) > expected_output_temp_flag.md5
-
 # Check whether STAR produces expected alignments
 # STAR alignments need to be fully within ground truth alignments for tests to pass; not checking 
 # vice versa because processing might cut off parts of reads (if testing STAR directly, add '-f 1' 

tests/test_integration_workflow_multiple_lanes/test.local.sh

@@ -42,8 +42,6 @@ find results/ -type f -name \*\.gz -exec gunzip '{}' \;
 find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
 md5sum --check "expected_output.md5"
 
-
-
 # Check whether STAR produces expected alignments
 # STAR alignments need to be fully within ground truth alignments for tests to pass; not checking 
 # vice versa because processing might cut off parts of reads (if testing STAR directly, add '-f 1' 
@@ -74,4 +72,3 @@ diff \
 diff \
     <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
     <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
-

tests/test_integration_workflow_multiple_lanes/test.slurm.sh

@@ -42,17 +42,6 @@ find results/ -type f -name \*\.gz -exec gunzip '{}' \;
 find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
 md5sum --check "expected_output.md5"
 
-# Checksum file generated with
-# find results/ \
-#     -type f \
-#     -name \*\.gz \
-#     -exec gunzip '{}' \;
-# find results/ \
-#     -type f \
-#     -name \*\.zip \
-#     -exec sh -c 'unzip -o {} -d $(dirname {})' \;
-# md5sum $(cat expected_output.files) > expected_output.md5
-
 # Check whether STAR produces expected alignments
 # STAR alignments need to be fully within ground truth alignments for tests to pass; not checking 
 # vice versa because processing might cut off parts of reads (if testing STAR directly, add '-f 1' 
@@ -83,5 +72,3 @@ diff \
 diff \
     <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
     <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
-
-

tests/test_integration_workflow_with_conda/test.local.sh

@@ -42,17 +42,6 @@ find results/ -type f -name \*\.gz -exec gunzip '{}' \;
 find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
 md5sum --check "expected_output.md5"
 
-# Checksum file generated with
-#find results/ \
-#    -type f \
-#    -name \*\.gz \
-#    -exec gunzip '{}' \;
-#find results/ \
-#    -type f \
-#    -name \*\.zip \
-#    -exec sh -c 'unzip -o {} -d $(dirname {})' \;
-#md5sum $(cat expected_output.files) > expected_output.md5
-
 # Check whether STAR produces expected alignments
 # STAR alignments need to be fully within ground truth alignments for tests to pass; not checking 
 # vice versa because processing might cut off parts of reads (if testing STAR directly, add '-f 1' 
@@ -83,4 +72,3 @@ diff \
 diff \
     <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
     <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
-

tests/test_integration_workflow_with_conda/test.slurm.sh

@@ -42,17 +42,6 @@ find results/ -type f -name \*\.gz -exec gunzip '{}' \;
 find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
 md5sum --check "expected_output.md5"
 
-# Checksum file generated with
-# find results/ \
-#     -type f \
-#     -name \*\.gz \
-#     -exec gunzip '{}' \;
-# find results/ \
-#     -type f \
-#     -name \*\.zip \
-#     -exec sh -c 'unzip -o {} -d $(dirname {})' \;
-# md5sum $(cat expected_output.files) > expected_output.md5
-
 # Check whether STAR produces expected alignments
 # STAR alignments need to be fully within ground truth alignments for tests to pass; not checking 
 # vice versa because processing might cut off parts of reads (if testing STAR directly, add '-f 1' 
@@ -83,5 +72,3 @@ diff \
 diff \
     <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
     <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
-
-

tests/test_sra_download_with_conda/test.local.sh

@@ -32,8 +32,6 @@ snakemake --snakefile="../../workflow/rules/sra_download.smk" \
                    log_dir="logs" \
                    cluster_log_dir="logs/cluster_log"
 
-
-
 # Check md5 sum of some output files
 find results/ -type f -name \*\.gz -exec gunzip '{}' \;
 find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;

tests/test_sra_download_with_conda/test.slurm.sh

@@ -31,7 +31,6 @@ snakemake --snakefile="../../workflow/rules/sra_download.smk" \
                    samples_out="results/sra_downloads/sra_samples.out.tsv" \
                    log_dir="logs" \
                    cluster_log_dir="logs/cluster_log"
-
 
 # Check md5 sum of some output files
 find results/ -type f -name \*\.gz -exec gunzip '{}' \;