Built site for gh-pages

.nojekyll

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-bebaa4a0
+d79de239

04_launch.html

@@ -280,8 +280,8 @@ <h2 class="anchored" data-anchor-id="local-execution">Local execution</h2>
 <div class="cell-output cell-output-stdout">
 <pre><code>N E X T F L O W  ~  version 24.10.0
 WARN: It appears you have never run this project before -- Option `-resume` is ignored
-Launching `nf-nest/examples/hello.nf` [nostalgic_carson] DSL2 - revision: 9d1a692a7e
-[96/869cf0] Submitted process &gt; hello
+Launching `nf-nest/examples/hello.nf` [grave_allen] DSL2 - revision: 9d1a692a7e
+[b5/8ac5f1] Submitted process &gt; hello
 Hello world!</code></pre>
 </div>
 </div>
@@ -294,8 +294,8 @@ <h2 class="anchored" data-anchor-id="cluster-execution">Cluster execution</h2>
 <div class="sourceCode cell-code" id="cb4"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="ex">./nextflow</span> run nf-nest/examples/hello.nf <span class="at">-profile</span> cluster </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>N E X T F L O W  ~  version 24.10.0
-Launching `nf-nest/examples/hello.nf` [evil_ardinghelli] DSL2 - revision: 9d1a692a7e
-[96/869cf0] Cached process &gt; hello
+Launching `nf-nest/examples/hello.nf` [romantic_solvay] DSL2 - revision: 9d1a692a7e
+[b5/8ac5f1] Cached process &gt; hello
 Hello world!</code></pre>
 </div>
 </div>

05_pkg.html

@@ -299,9 +299,9 @@ <h2 class="anchored" data-anchor-id="precompilation-on-hpc">Precompilation on HP
 <span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a><span class="ex">./nextflow</span> run nf-nest/pkg.nf <span class="at">-profile</span> cluster</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>N E X T F L O W  ~  version 24.10.0
-Launching `nf-nest/pkg.nf` [stupefied_goldstine] DSL2 - revision: fc0374e695
-[d2/2d9cfa] Submitted process &gt; instantiate_process
-[08/cabe06] Submitted process &gt; precompile</code></pre>
+Launching `nf-nest/pkg.nf` [golden_shaw] DSL2 - revision: fc0374e695
+[9b/6b6098] Submitted process &gt; instantiate_process
+[bf/bbd094] Submitted process &gt; precompile</code></pre>
 </div>
 </div>
 <p>Optionally, you can append an argument to specify the number of threads to request and use during pre-compilation: e.g.&nbsp;add <code>--nPrecompileThreads 20</code> to request 20 threads instead of the default of 10.</p>

06_cross_product.html

@@ -345,43 +345,43 @@ <h2 class="anchored" data-anchor-id="running-the-script">Running the script</h2>
 <div class="cell-output cell-output-stdout">
 <pre><code>N E X T F L O W  ~  version 24.10.0
 WARN: It appears you have never run this project before -- Option `-resume` is ignored
-Launching `nf-nest/examples/many_jobs.nf` [nauseous_volta] DSL2 - revision: aa082b1978
-[cf/316661] Submitted process &gt; run_julia (7)
-[98/3f89f3] Submitted process &gt; run_julia (16)
-[f5/9200b5] Submitted process &gt; run_julia (8)
-[60/79d084] Submitted process &gt; run_julia (10)
-[25/304afb] Submitted process &gt; run_julia (12)
-[dc/f8a7cb] Submitted process &gt; run_julia (1)
-[23/a921d6] Submitted process &gt; run_julia (6)
-[17/60efee] Submitted process &gt; run_julia (3)
-[fe/d3775a] Submitted process &gt; run_julia (2)
-[23/02e5a5] Submitted process &gt; run_julia (11)
-[61/92282e] Submitted process &gt; run_julia (9)
-[d2/4f9929] Submitted process &gt; run_julia (13)
-[c5/278d1e] Submitted process &gt; run_julia (5)
-[ec/ca8573] Submitted process &gt; run_julia (15)
-[b9/99bc51] Submitted process &gt; run_julia (4)
-[a7/6c5a96] Submitted process &gt; run_julia (14)
-[ff/2ee016] Submitted process &gt; run_julia (17)
-[ba/85000e] Submitted process &gt; run_julia (18)
+Launching `nf-nest/examples/many_jobs.nf` [pensive_cuvier] DSL2 - revision: aa082b1978
+[9a/f95c38] Submitted process &gt; run_julia (16)
+[31/c84da1] Submitted process &gt; run_julia (8)
+[70/882e38] Submitted process &gt; run_julia (7)
+[f8/827180] Submitted process &gt; run_julia (9)
+[40/502eb0] Submitted process &gt; run_julia (5)
+[24/235871] Submitted process &gt; run_julia (13)
+[08/c3250a] Submitted process &gt; run_julia (3)
+[2a/d590b5] Submitted process &gt; run_julia (11)
+[1a/18653d] Submitted process &gt; run_julia (6)
+[ba/2ffe85] Submitted process &gt; run_julia (2)
+[4f/48bab2] Submitted process &gt; run_julia (4)
+[55/fb4a96] Submitted process &gt; run_julia (14)
+[6b/ba0d04] Submitted process &gt; run_julia (15)
+[33/3c91f1] Submitted process &gt; run_julia (1)
+[67/d912ab] Submitted process &gt; run_julia (12)
+[42/edc64d] Submitted process &gt; run_julia (10)
+[d0/25bfed] Submitted process &gt; run_julia (18)
+[39/75210b] Submitted process &gt; run_julia (17)
+3 * 2 = 6
+2 + 2 = 4
 2 + 1 = 3
 2 * 1 = 2
-3 * 2 = 6
-2 * 2 = 4
-2 * 3 = 6
-1 + 1 = 2
-1 * 3 = 3
+1 + 3 = 4
+3 + 1 = 4
 1 + 2 = 3
-1 * 1 = 1
 2 + 3 = 5
-2 + 2 = 4
-3 + 1 = 4
-1 + 3 = 4
-3 + 2 = 5
+1 * 3 = 3
+1 * 1 = 1
 1 * 2 = 2
 3 * 1 = 3
-3 + 3 = 6
-3 * 3 = 9</code></pre>
+3 + 2 = 5
+1 + 1 = 2
+2 * 3 = 6
+2 * 2 = 4
+3 * 3 = 9
+3 + 3 = 6</code></pre>
 </div>
 </div>
 

07_combine.html

@@ -341,33 +341,33 @@ <h2 class="anchored" data-anchor-id="running-the-nextflow-script">Running the ne
 <span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="ex">./nextflow</span> run nf-nest/examples/full.nf <span class="at">-profile</span> cluster </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>N E X T F L O W  ~  version 24.10.0
-Launching `nf-nest/examples/full.nf` [agitated_knuth] DSL2 - revision: a68c131baa
-[6d/3357a5] Submitted process &gt; combine_workflow:instantiate_process
-[25/d08519] Submitted process &gt; instantiate_process
-[bb/03d46d] Submitted process &gt; combine_workflow:precompile
-[bb/605315] Submitted process &gt; precompile
-[fa/aa7751] Submitted process &gt; run_julia (9)
-[7b/150dd2] Submitted process &gt; run_julia (8)
-[cd/7a1c39] Submitted process &gt; run_julia (2)
-[df/ffce39] Submitted process &gt; run_julia (13)
-[c8/23f9a2] Submitted process &gt; run_julia (12)
-[b6/ed34c6] Submitted process &gt; run_julia (4)
-[7f/32c560] Submitted process &gt; run_julia (5)
-[23/dca8ec] Submitted process &gt; run_julia (15)
-[3e/bd5153] Submitted process &gt; run_julia (14)
-[8f/1b5deb] Submitted process &gt; run_julia (10)
-[57/f522b3] Submitted process &gt; run_julia (6)
-[60/eb9c28] Submitted process &gt; run_julia (11)
-[9c/ce18ab] Submitted process &gt; run_julia (1)
-[13/599d3d] Submitted process &gt; run_julia (7)
-[cb/d8f2f4] Submitted process &gt; run_julia (3)
-[e0/fad42d] Submitted process &gt; run_julia (16)
-[34/e101c3] Submitted process &gt; run_julia (17)
-[3b/a775ca] Submitted process &gt; run_julia (18)
-[90/4f63ff] Submitted process &gt; run_julia (20)
-[65/b68f71] Submitted process &gt; run_julia (19)
-[4a/d5b369] Submitted process &gt; combine_workflow:combine_process
-[21/1bfa99] Submitted process &gt; plot</code></pre>
+Launching `nf-nest/examples/full.nf` [intergalactic_jepsen] DSL2 - revision: a68c131baa
+[9c/0659ed] Submitted process &gt; combine_workflow:instantiate_process
+[71/d2fadf] Submitted process &gt; instantiate_process
+[ce/f1a696] Submitted process &gt; combine_workflow:precompile
+[4d/72b110] Submitted process &gt; precompile
+[42/0732cc] Submitted process &gt; run_julia (9)
+[5e/81171f] Submitted process &gt; run_julia (1)
+[c5/1ccbfe] Submitted process &gt; run_julia (3)
+[d4/228929] Submitted process &gt; run_julia (4)
+[2b/2baf59] Submitted process &gt; run_julia (14)
+[8c/2bb063] Submitted process &gt; run_julia (15)
+[d5/5001bb] Submitted process &gt; run_julia (13)
+[56/de7ec7] Submitted process &gt; run_julia (7)
+[ab/d18893] Submitted process &gt; run_julia (11)
+[76/fc81a9] Submitted process &gt; run_julia (5)
+[69/6f13e4] Submitted process &gt; run_julia (10)
+[28/fa731e] Submitted process &gt; run_julia (2)
+[61/f7b16b] Submitted process &gt; run_julia (12)
+[8e/3df7d5] Submitted process &gt; run_julia (16)
+[d3/fe1273] Submitted process &gt; run_julia (6)
+[56/f5fc6a] Submitted process &gt; run_julia (8)
+[ee/683820] Submitted process &gt; run_julia (17)
+[58/7fa150] Submitted process &gt; run_julia (18)
+[28/2a8382] Submitted process &gt; run_julia (19)
+[c2/f5b56b] Submitted process &gt; run_julia (20)
+[52/031bf9] Submitted process &gt; combine_workflow:combine_process
+[c0/9912ef] Submitted process &gt; plot</code></pre>
 </div>
 </div>
 </section>
@@ -388,7 +388,7 @@ <h3 class="anchored" data-anchor-id="organizing-the-output-with-a-publishdir">Or
 <div class="sourceCode cell-code" id="cb6"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="ex">tree</span> experiment_repo/deliverables</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>experiment_repo/deliverables
-└── scriptName=full.nf___runName=agitated_knuth
+└── scriptName=full.nf___runName=intergalactic_jepsen
     ├── output
     │&nbsp;&nbsp; ├── summary.csv
     │&nbsp;&nbsp; └── swap_prs.csv
@@ -402,11 +402,11 @@ <h3 class="anchored" data-anchor-id="organizing-the-output-with-a-publishdir">Or
 <div class="sourceCode cell-code" id="cb8"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> experiment_repo</span>
 <span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a><span class="ex">./nextflow</span> log</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
-<pre><code>TIMESTAMP           DURATION    RUN NAME            STATUS  REVISION ID SESSION ID                              COMMAND                                                
-2024-11-12 07:05:30 3.2s        nostalgic_carson    OK      9d1a692a7e  317a6835-37ee-4f54-9d9f-b0df69f57bbd    nextflow run nf-nest/examples/hello.nf                 
-2024-11-12 07:05:36 7.6s        evil_ardinghelli    OK      9d1a692a7e  317a6835-37ee-4f54-9d9f-b0df69f57bbd    nextflow run nf-nest/examples/hello.nf -profile cluster
-2024-11-12 07:06:32 1m 22s      stupefied_goldstine OK      fc0374e695  317a6835-37ee-4f54-9d9f-b0df69f57bbd    nextflow run nf-nest/pkg.nf -profile cluster           
-2024-11-12 07:08:17 4m 33s      agitated_knuth      OK      a68c131baa  317a6835-37ee-4f54-9d9f-b0df69f57bbd    nextflow run nf-nest/examples/full.nf -profile cluster </code></pre>
+<pre><code>TIMESTAMP           DURATION    RUN NAME                STATUS  REVISION ID SESSION ID                              COMMAND                                                
+2024-11-12 09:04:09 3.5s        grave_allen             OK      9d1a692a7e  bf02b0fb-fa7d-4171-88a3-e89239ee4248    nextflow run nf-nest/examples/hello.nf                 
+2024-11-12 09:04:16 6.9s        romantic_solvay         OK      9d1a692a7e  bf02b0fb-fa7d-4171-88a3-e89239ee4248    nextflow run nf-nest/examples/hello.nf -profile cluster
+2024-11-12 09:05:11 1m 13s      golden_shaw             OK      fc0374e695  bf02b0fb-fa7d-4171-88a3-e89239ee4248    nextflow run nf-nest/pkg.nf -profile cluster           
+2024-11-12 09:06:48 3m 8s       intergalactic_jepsen    OK      a68c131baa  bf02b0fb-fa7d-4171-88a3-e89239ee4248    nextflow run nf-nest/examples/full.nf -profile cluster </code></pre>
 </div>
 </div>
 

08_containers.html

@@ -339,11 +339,11 @@ <h2 class="anchored" data-anchor-id="using-an-existing-container">Using an exist
 <span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a><span class="ex">./nextflow</span> run nf-nest/examples/stan_example.nf <span class="at">-profile</span> cluster</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>N E X T F L O W  ~  version 24.10.0
-Launching `nf-nest/examples/stan_example.nf` [kickass_northcutt] DSL2 - revision: 8cef9f29d6
+Launching `nf-nest/examples/stan_example.nf` [festering_khorana] DSL2 - revision: 8cef9f29d6
 WARN: Apptainer cache directory has not been defined -- Remote image will be stored in the path: /arc/burst/st-alexbou-1/abc/nf-nest-doc/experiment_repo/work/singularity -- Use the environment variable NXF_APPTAINER_CACHEDIR to specify a different location
 Pulling Apptainer image docker://alexandrebouchardcote/default:0.1.6 [cache /arc/burst/st-alexbou-1/abc/nf-nest-doc/experiment_repo/work/singularity/alexandrebouchardcote-default-0.1.6.img]
-[0b/5344f6] Submitted process &gt; compile_stan
-[9b/4fd335] Submitted process &gt; run_stan</code></pre>
+[0d/7c12aa] Submitted process &gt; compile_stan
+[04/d00cdc] Submitted process &gt; run_stan</code></pre>
 </div>
 </div>
 </section>

09_gpu.html

@@ -254,9 +254,9 @@ <h2 class="anchored" data-anchor-id="installing-cuda.jl">Installing CUDA.jl</h2>
 <span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="ex">./nextflow</span> run nf-nest/pkg_gpu.nf </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>N E X T F L O W  ~  version 24.10.0
-Launching `nf-nest/pkg_gpu.nf` [insane_monod] DSL2 - revision: 713b74ac4a
-[0a/d32c39] Submitted process &gt; instantiate_process
-[9a/f339af] Submitted process &gt; precompile_gpu</code></pre>
+Launching `nf-nest/pkg_gpu.nf` [hopeful_turing] DSL2 - revision: 713b74ac4a
+[b6/0ba7e0] Submitted process &gt; instantiate_process
+[70/2ce6ba] Submitted process &gt; precompile_gpu</code></pre>
 </div>
 </div>
 </section>
@@ -303,16 +303,16 @@ <h2 class="anchored" data-anchor-id="running-nextflow-processes-requiring-gpu">R
 <span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a><span class="ex">./nextflow</span> run nf-nest/examples/gpu.nf <span class="at">-profile</span> cluster</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>N E X T F L O W  ~  version 24.10.0
-Launching `nf-nest/examples/gpu.nf` [sick_legentil] DSL2 - revision: 9be41cea49
-[70/537eb2] Submitted process &gt; instantiate_process
-[d4/f4b844] Submitted process &gt; precompile_gpu
-[05/4b36e9] Submitted process &gt; run_julia
+Launching `nf-nest/examples/gpu.nf` [thirsty_mahavira] DSL2 - revision: 9be41cea49
+[b6/49dd3e] Submitted process &gt; instantiate_process
+[80/583246] Submitted process &gt; precompile_gpu
+[fc/7402e7] Submitted process &gt; run_julia
 CPU
- 15.295592 seconds (4.79 M allocations: 517.701 MiB, 4.03% gc time, 18.96% compilation time)
- 12.138829 seconds (2 allocations: 190.735 MiB, 0.06% gc time)
+ 13.046295 seconds (4.79 M allocations: 517.701 MiB, 3.56% gc time, 17.49% compilation time)
+ 10.582634 seconds (2 allocations: 190.735 MiB, 0.10% gc time)
 GPU
-  1.972740 seconds (1.67 M allocations: 107.375 MiB, 95.51% compilation time)
-  0.000784 seconds (50 allocations: 1.172 KiB)
+  1.535394 seconds (1.67 M allocations: 107.375 MiB, 96.04% compilation time)
+  0.000591 seconds (50 allocations: 1.172 KiB)
 CUDA runtime 12.5, artifact installation
 CUDA driver 12.6
 NVIDIA driver 550.90.12
@@ -339,7 +339,7 @@ <h2 class="anchored" data-anchor-id="running-nextflow-processes-requiring-gpu">R
 - CUDA_Runtime_jll.version: 12.5
 
 1 device:
-  0: Tesla V100-SXM2-16GB (sm_70, 15.171 GiB / 16.000 GiB available)</code></pre>
+  0: Tesla V100-SXM2-32GB (sm_70, 31.137 GiB / 32.000 GiB available)</code></pre>
 </div>
 </div>
 </section>