Merge branch 'update.containers' into 'develop'

Update.containers See merge request !73

Merge branch 'update.containers' into 'develop'
Update.containers See merge request !73
f2425d63 · Gervaise Henry · ec949139 · 83add5e0 · ec949139 · f2425d63
Commit f2425d63 authored 4 years ago by Gervaise Henry
--- a/docs/dag.png
+++ b/docs/dag.png
--- a/docs/references.md
+++ b/docs/references.md
@@ -4,28 +4,28 @@
  * Anaconda (Anaconda Software Distribution, [https://anaconda.com](https://anaconda.com))

 2. **DERIVA**:
-  * Bugacov, A., Czajkowski, K., Kesselman, C., Kumar,  A., Schuler, R. E. and Tangmunarunkit, H. 2017 Experiences with DERIVA: An Asset Management Platform for Accelerating eScience. IEEE 13th International Conference on e-Science (e-Science), Auckland, 2017, pp. 79-88, doi:[10.1109/eScience.2017.20](https://doi.org/10.1109/eScience.2017.20).
+  * Bugacov, A., Czajkowski, K., Kesselman, C., Kumar, A., Schuler, R. E., & Tangmunarunkit, H. (2017, October). Experiences with DERIVA: An asset management platform for accelerating eScience. In 2017 IEEE 13th International Conference on e-Science (e-Science) (pp. 79-88). IEEE. doi:[10.1109/eScience.2017.20](https://doi.org/10.1109/eScience.2017.20).

 3. **BDBag**:  
-  * D'Arcy, M., Chard, K., Foster, I., Kesselman, C., Madduri, R., Saint, N., & Wagner, R.. 2019. Big Data Bags: A Scalable Packaging Format for Science. Zenodo. doi:[10.5281/zenodo.3338725](http://doi.org/10.5281/zenodo.3338725).
+  * Madduri, R., Chard, K., DArcy, M., Jung, S. C., Rodriguez, A., Sulakhe, D., ... & Foster, I. (2019). Reproducible big data science: A case study in continuous FAIRness. PloS one, 14(4), e0213013. doi:[10.1371/journal.pone.0213013](https://doi.org/10.1371/journal.pone.0213013).

 4. **trimgalore**:
  * trimgalore [https://github.com/FelixKrueger/TrimGalore](https://github.com/FelixKrueger/TrimGalore)

 5. **hisat2**:
-  * Kim ,D.,Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L. 2019 Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. Aug;37(8):907-915. doi:[10.1038/s41587-019-0201-4](https://doi.org/10.1038/s41587-019-0201-4).
+  * Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature biotechnology, 37(8), 907-915. doi:[10.1038/s41587-019-0201-4](https://doi.org/10.1038/s41587-019-0201-4).

 6. **samtools**:
-  * Li H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25: 2078-9. doi:[10.1093/bioinformatics/btp352](http://dx.doi.org/10.1093/bioinformatics/btp352)
+  * Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., ... & Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:[10.1093/bioinformatics/btp352](http://dx.doi.org/10.1093/bioinformatics/btp352)

 7. **picard**:
  * “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. [http://broadinstitute.github.io/picard/](http://broadinstitute.github.io/picard/); Broad Institute

 8. **featureCounts**:
-  * Liao, Y., Smyth, G.K., Shi, W. 2014 featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. Apr 1;30(7):923-30. doi:[10.1093/bioinformatics/btt656](https://doi.org/10.1093/bioinformatics/btt656).
+  * Liao, Y., Smyth, G. K., & Shi, W. (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923-930. doi:[10.1093/bioinformatics/btt656](https://doi.org/10.1093/bioinformatics/btt656).

 9. **deeptools**:
-  * Ramírez, F., D. P. Ryan, B. Grüning, V. Bhardwaj, F. Kilpert, A. S. Richter, S. Heyne, F. Dündar, and T. Manke. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research 44: W160-165. doi:[10.1093/nar/gkw257](http://dx.doi.org/10.1093/nar/gkw257)
+  * Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., ... & Manke, T. (2016). deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic acids research, 44(W1), W160-W165. doi:[10.1093/nar/gkw257](http://dx.doi.org/10.1093/nar/gkw257)

 10. **Seqtk**:
  * Seqtk [https://github.com/lh3/seqtk](https://github.com/lh3/seqtk)
@@ -37,13 +37,13 @@
  * FastQC [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

 13. **SeqWho**
-  * SeqWho [https://git.biohpc.swmed.edu/s181649/seqwho](https://git.biohpc.swmed.edu/s181649/seqwho)
+  * Bennett, C., Thornton, M., Park, C., Henry, G., Zhang, Y., Malladi, V. S., & Kim, D. (2021). SeqWho: Reliable, rapid determination of sequence file identity using k-mer frequencies. bioRxiv, 2021.2003.2010.434827. doi:[10.1101/2021.03.10.434827](https://doi.org/10.1101/2021.03.10.434827)

 14. **RSeQC**:
  * Wang, L., Wang, S., Li, W. 2012 RSeQC: quality control of RNA-seq experiments. Bioinformatics. Aug 15;28(16):2184-5. doi:[10.1093/bioinformatics/bts356](https://doi.org/10.1093/bioinformatics/bts356).

 15. **MultiQC**:
-  * Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354)
+  * Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047-3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354)

 16. **Nextflow**:
-  * Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., and Notredame, C. 2017. Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316.
\ No newline at end of file
+  * Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316-319.
\ No newline at end of file
--- a/docs/software_references_mqc.yaml
+++ b/docs/software_references_mqc.yaml
@@ -16,14 +16,14 @@
                <li><strong>DERIVA</strong>:</li>
                </ol>
                <ul>
-                <li>Bugacov, A., Czajkowski, K., Kesselman, C., Kumar, A., Schuler, R. E. and Tangmunarunkit, H. 2017 Experiences with DERIVA: An Asset Management Platform for Accelerating eScience. IEEE 13th International Conference on e-Science (e-Science), Auckland, 2017, pp. 79-88, doi:<a href="https://doi.org/10.1109/eScience.2017.20">10.1109/eScience.2017.20</a>.</li>
+                <li>Bugacov, A., Czajkowski, K., Kesselman, C., Kumar, A., Schuler, R. E., &amp; Tangmunarunkit, H. (2017, October). Experiences with DERIVA: An asset management platform for accelerating eScience. In 2017 IEEE 13th International Conference on e-Science (e-Science) (pp. 79-88). IEEE. doi:<a href="https://doi.org/10.1109/eScience.2017.20">10.1109/eScience.2017.20</a>.</li>
                </ul>
                <ol start="3" style="list-style-type: decimal">
                <li><strong>BDBag</strong>:<br />
                </li>
                </ol>
                <ul>
-                <li>D'Arcy, M., Chard, K., Foster, I., Kesselman, C., Madduri, R., Saint, N., &amp; Wagner, R.. 2019. Big Data Bags: A Scalable Packaging Format for Science. Zenodo. doi:<a href="http://doi.org/10.5281/zenodo.3338725">10.5281/zenodo.3338725</a>.</li>
+                <li>Madduri, R., Chard, K., DArcy, M., Jung, S. C., Rodriguez, A., Sulakhe, D., ... &amp; Foster, I. (2019). Reproducible big data science: A case study in continuous FAIRness. PloS one, 14(4), e0213013. doi:<a href="https://doi.org/10.1371/journal.pone.0213013">10.1371/journal.pone.0213013</a>.</li>
                </ul>
                <ol start="4" style="list-style-type: decimal">
                <li><strong>trimgalore</strong>:</li>
@@ -35,13 +35,13 @@
                <li><strong>hisat2</strong>:</li>
                </ol>
                <ul>
-                <li>Kim ,D.,Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L. 2019 Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. Aug;37(8):907-915. doi:<a href="https://doi.org/10.1038/s41587-019-0201-4">10.1038/s41587-019-0201-4</a>.</li>
+                <li>Kim, D., Paggi, J. M., Park, C., Bennett, C., &amp; Salzberg, S. L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature biotechnology, 37(8), 907-915. doi:<a href="https://doi.org/10.1038/s41587-019-0201-4">10.1038/s41587-019-0201-4</a>.</li>
                </ul>
                <ol start="6" style="list-style-type: decimal">
                <li><strong>samtools</strong>:</li>
                </ol>
                <ul>
-                <li>Li H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25: 2078-9. doi:<a href="http://dx.doi.org/10.1093/bioinformatics/btp352">10.1093/bioinformatics/btp352</a></li>
+                <li>Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., ... &amp; Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:<a href="http://dx.doi.org/10.1093/bioinformatics/btp352">10.1093/bioinformatics/btp352</a></li>
                </ul>
                <ol start="7" style="list-style-type: decimal">
                <li><strong>picard</strong>:</li>
@@ -53,13 +53,13 @@
                <li><strong>featureCounts</strong>:</li>
                </ol>
                <ul>
-                <li>Liao, Y., Smyth, G.K., Shi, W. 2014 featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. Apr 1;30(7):923-30. doi:<a href="https://doi.org/10.1093/bioinformatics/btt656">10.1093/bioinformatics/btt656</a>.</li>
+                <li>Liao, Y., Smyth, G. K., &amp; Shi, W. (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923-930. doi:<a href="https://doi.org/10.1093/bioinformatics/btt656">10.1093/bioinformatics/btt656</a>.</li>
                </ul>
                <ol start="9" style="list-style-type: decimal">
                <li><strong>deeptools</strong>:</li>
                </ol>
                <ul>
-                <li>Ramírez, F., D. P. Ryan, B. Grüning, V. Bhardwaj, F. Kilpert, A. S. Richter, S. Heyne, F. Dündar, and T. Manke. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research 44: W160-165. doi:<a href="http://dx.doi.org/10.1093/nar/gkw257">10.1093/nar/gkw257</a></li>
+                <li>Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., ... &amp; Manke, T. (2016). deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic acids research, 44(W1), W160-W165. doi:<a href="http://dx.doi.org/10.1093/nar/gkw257">10.1093/nar/gkw257</a></li>
                </ul>
                <ol start="10" style="list-style-type: decimal">
                <li><strong>Seqtk</strong>:</li>
@@ -83,7 +83,7 @@
                <li><strong>SeqWho</strong></li>
                </ol>
                <ul>
-                <li>SeqWho <a href="https://git.biohpc.swmed.edu/s181649/seqwho" class="uri">https://git.biohpc.swmed.edu/s181649/seqwho</a></li>
+                <li>Bennett, C., Thornton, M., Park, C., Henry, G., Zhang, Y., Malladi, V. S., &amp; Kim, D. (2021). SeqWho: Reliable, rapid determination of sequence file identity using k-mer frequencies. bioRxiv, 2021.2003.2010.434827. doi:<a href="https://doi.org/10.1101/2021.03.10.434827">10.1101/2021.03.10.434827</a></li>
                </ul>
                <ol start="14" style="list-style-type: decimal">
                <li><strong>RSeQC</strong>:</li>
@@ -95,11 +95,11 @@
                <li><strong>MultiQC</strong>:</li>
                </ol>
                <ul>
-                <li>Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:<a href="https://dx.doi.org/10.1093/bioinformatics/btw354">10.1093/bioinformatics/btw354</a></li>
+                <li>Ewels, P., Magnusson, M., Lundin, S., &amp; Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047-3048. doi:<a href="https://dx.doi.org/10.1093/bioinformatics/btw354">10.1093/bioinformatics/btw354</a></li>
                </ul>
                <ol start="16" style="list-style-type: decimal">
                <li><strong>Nextflow</strong>:</li>
                </ol>
                <ul>
-                <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., and Notredame, C. 2017. Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316.</li>
+                <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., &amp; Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316-319.</li>
                </ul>
--- a/nextflow.config
+++ b/nextflow.config
@@ -44,7 +44,7 @@ process {
    container = 'gudmaprbk/fastqc0.11.9:1.0.1'
  }
  withName:seqwho {
-    container = 'gudmaprbk/seqwho0.0.1:1.0.0'
+    container = 'gudmaprbk/seqwho1.0.0:1.0.0'
  }
  withName:trimData {
    container = 'gudmaprbk/trimgalore0.6.6:1.0.0'

--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -720,13 +720,13 @@ process seqwho {
    echo -e "LOG: seqwho ran" >> ${repRID}.seqwho.log

    # parse inference from R1
-    speciesR1=\$(cat SeqWho_call.tsv | grep ${fastq[0]} | cut -f17 -d\$'\t' | cut -f2 -d":" | tr -d " ")
-    seqtypeR1=\$(cat SeqWho_call.tsv | grep ${fastq[0]} | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
-    confidenceR1=\$(cat SeqWho_call.tsv | grep ${fastq[0]} | cut -f16 -d\$'\t' | cut -f2 -d":" | tr -d " ")
+    speciesR1=\$(cat SeqWho_call.tsv | grep ${fastq[0]} | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
+    seqtypeR1=\$(cat SeqWho_call.tsv | grep ${fastq[0]} | cut -f19 -d\$'\t' | cut -f2 -d":" | tr -d " ")
+    confidenceR1=\$(cat SeqWho_call.tsv | grep ${fastq[0]} | cut -f17 -d\$'\t' | cut -f2 -d":" | tr -d " ")
    if [ "\${confidenceR1}" == "low" ]
    then
-      speciesConfidenceR1=\$(cat SeqWho_call.tsv | grep ${fastq[0]} | cut -f16 -d\$'\t' | cut -f3 -d":" | tr -d " ")
-      seqtypeConfidenceR1=\$(cat SeqWho_call.tsv | grep ${fastq[0]} | cut -f16 -d\$'\t' | cut -f4 -d":" | tr -d " ")
+      speciesConfidenceR1=\$(cat SeqWho_call.tsv | grep ${fastq[0]} | cut -f17 -d\$'\t' | cut -f3 -d":" | tr -d " ")
+      seqtypeConfidenceR1=\$(cat SeqWho_call.tsv | grep ${fastq[0]} | cut -f17 -d\$'\t' | cut -f4 -d":" | tr -d " ")
    else
      speciesConfidenceR1="1"
      seqtypeConfidenceR1="1"
@@ -736,13 +736,13 @@ process seqwho {
    # parse inference from R2
    if [ "${ends}" == "pe" ]
    then
-      speciesR2=\$(cat SeqWho_call.tsv | grep ${fastq[1]} | cut -f17 -d\$'\t' | cut -f2 -d":" | tr -d " ")
-      seqtypeR2=\$(cat SeqWho_call.tsv | grep ${fastq[1]} | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
-      confidenceR2=\$(cat SeqWho_call.tsv | grep ${fastq[1]} | cut -f16 -d\$'\t' | cut -f2 -d":" | tr -d " ")
+      speciesR2=\$(cat SeqWho_call.tsv | grep ${fastq[1]} | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
+      seqtypeR2=\$(cat SeqWho_call.tsv | grep ${fastq[1]} | cut -f19 -d\$'\t' | cut -f2 -d":" | tr -d " ")
+      confidenceR2=\$(cat SeqWho_call.tsv | grep ${fastq[1]} | cut -f17 -d\$'\t' | cut -f2 -d":" | tr -d " ")
      if [ "\${confidenceR2}" == "low" ]
      then
-        speciesConfidenceR2=\$(cat SeqWho_call.tsv | grep ${fastq[1]} | cut -f16 -d\$'\t' | cut -f3 -d":" | tr -d " ")
-        seqtypeConfidenceR2=\$(cat SeqWho_call.tsv | grep ${fastq[1]} | cut -f16 -d\$'\t' | cut -f4 -d":" | tr -d " ")
+        speciesConfidenceR2=\$(cat SeqWho_call.tsv | grep ${fastq[1]} | cut -f17 -d\$'\t' | cut -f3 -d":" | tr -d " ")
+        seqtypeConfidenceR2=\$(cat SeqWho_call.tsv | grep ${fastq[1]} | cut -f17 -d\$'\t' | cut -f4 -d":" | tr -d " ")
      else
        speciesConfidenceR2="1"
        seqtypeConfidenceR2="1"
@@ -857,9 +857,9 @@ process seqwho {
      gzip sampled.1.seed300.fastq &
      wait
      seqwho.py -f sampled.1.seed*.fastq.gz -x SeqWho.ix
-      seqtypeR1_1=\$(cat SeqWho_call.tsv | grep sampled.1.seed100.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
-      seqtypeR1_2=\$(cat SeqWho_call.tsv | grep sampled.1.seed200.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
-      seqtypeR1_3=\$(cat SeqWho_call.tsv | grep sampled.1.seed300.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
+      seqtypeR1_1=\$(cat SeqWho_call.tsv | grep sampled.1.seed100.fastq.gz | cut -f19 -d\$'\t' | cut -f2 -d":" | tr -d " ")
+      seqtypeR1_2=\$(cat SeqWho_call.tsv | grep sampled.1.seed200.fastq.gz | cut -f19 -d\$'\t' | cut -f2 -d":" | tr -d " ")
+      seqtypeR1_3=\$(cat SeqWho_call.tsv | grep sampled.1.seed300.fastq.gz | cut -f19 -d\$'\t' | cut -f2 -d":" | tr -d " ")
      cp SeqWho_call.tsv SeqWho_call_sampledR1.tsv
      if [ "\${seqtypeR1_1}" == "\${seqtypeR1}" ] && [ "\${seqtypeR1_2}" == "\${seqtypeR1}" ] && [ "\${seqtypeR1_3}" == "\${seqtypeR1}" ]
      then
@@ -878,9 +878,9 @@ process seqwho {
        gzip sampled.2.seed300.fastq &
        wait
        seqwho.py -f sampled.2.seed*.fastq.gz -x SeqWho.ix
-        seqtypeR2_1=\$(cat SeqWho_call.tsv | grep sampled.2.seed100.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
-        seqtypeR2_2=\$(cat SeqWho_call.tsv | grep sampled.2.seed200.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
-        seqtypeR2_3=\$(cat SeqWho_call.tsv | grep sampled.2.seed300.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
+        seqtypeR2_1=\$(cat SeqWho_call.tsv | grep sampled.2.seed100.fastq.gz | cut -f19 -d\$'\t' | cut -f2 -d":" | tr -d " ")
+        seqtypeR2_2=\$(cat SeqWho_call.tsv | grep sampled.2.seed200.fastq.gz | cut -f19 -d\$'\t' | cut -f2 -d":" | tr -d " ")
+        seqtypeR2_3=\$(cat SeqWho_call.tsv | grep sampled.2.seed300.fastq.gz | cut -f19 -d\$'\t' | cut -f2 -d":" | tr -d " ")
        cp SeqWho_call.tsv SeqWho_call_sampledR2.tsv
        if [ "\${seqtypeR2_1}" == "\${seqtypeR1}" ] && [ "\${seqtypeR2_2}" == "\${seqtypeR1}" ] && [ "\${seqtypeR2_3}" == "\${seqtypeR1}" ]
        then